|            |
|------------|
|            |  |  |
| (Mark One) |   |   |
| [X]        |   | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 |
|       |   | For the fiscal year ended: September 30, 2013 |
|       |   | OR |
| [  ]       |   | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 |
|       |   | For the transition period from ________________ to ________________ |

|                                                        |
|--------------------------------------------------------|
|                                                        |
| AMTECH SYSTEMS, INC.                                   |
| (Exact name of registrant as specified in its charter) |

|                                                               |
|---------------------------------------------------------------|
|                                                               |  |
| Arizona                                                       | 86-0411215 |
| (State or other jurisdiction ofincorporation or organization) | (I.R.S. EmployerIdentification No.) |
|                                                          |
| 131 South Clark Drive, Tempe, Arizona                         | 85281 |
| (Address of principal executive offices)                      | (Zip Code) |

|                                                             |
|-------------------------------------------------------------|
|                                                             |  |
| Registrant’s telephone number, including area code:   | 480-967-5146 |
|                                                        |   |
| Securities registered pursuant to Section 12(b) of the Act: |
| None                                                        |
|                                                        |
| Securities registered pursuant to Section 12(g) of the Act: |
| Title of Each Class                                         | Name of Each Exchange on Which Registered |
| Common Stock, $0.01 Par Value                               | The NASDAQ Stock Market LLC |

----

----

|                                                                                                         |
|---------------------------------------------------------------------------------------------------------|
|                                                                                                         |  |
| PART III                                                                                                | Page |
| ITEM 10. Directors, executive officers and governance                                                   | 4 |
| ITEM 11. Executive compensation                                                                         | 7 |
| ITEM 12. Security ownership of certain beneficial owners and management and related stockholder matters | 19 |
| ITEM 13. Certain relationships and related transactions, and director independence                      | 20 |
| ITEM 14. Principal accounting fees and services                                                         | 21 |
|                                                                                                    |   |
| PART IV                                                                                                 |   |
| ITEM 15. Exhibits, financial statement schedules                                                        | 22 |

----

|                      |
|----------------------|
|                      |  |  |
| Name                 | Age | Position with the Company |
| Jong S. Whang        | 68 | Executive Chairman and Director |
| Fokko Pentinga       | 58 | President, Chief Executive Officer and Director |
| Bradley C. Anderson  | 52 | Executive Vice President – Finance, Chief Financial Officer, Treasurer and Secretary |
| Michael Garnreiter   | 61 | Director |
| Alfred W. Giese      | 75 | Director |
| Egbert J. G. Goudena | 64 | Director |
| Robert F. King       | 80 | Director |

----

----

----

|         |                                                                                 |
|---------|---------------------------------------------------------------------------------|
| • | Jong S. Whang        Executive Chairman |

|         |                                                                                                     |
|---------|-----------------------------------------------------------------------------------------------------|
| • | Fokko Pentinga        President and Chief Executive Officer |

|         |                                                                                                                         |
|---------|-------------------------------------------------------------------------------------------------------------------------|
| • | Bradley C. Anderson        Executive Vice President and Chief Financial Officer |

|         |                                                                                                           |
|---------|-----------------------------------------------------------------------------------------------------------|
| • | Robert T. Hass        Vice President and Chief Accounting Officer |

|         |                                                                                                           |
|---------|-----------------------------------------------------------------------------------------------------------|
| • | Jeong Mo Hwang        Vice President and Chief Technology Officer |

----

|         |                                                                                                                      |
|---------|----------------------------------------------------------------------------------------------------------------------|
| • | align the interests of our executives and shareholders by rewarding executives when shareholder value increases; and |

|         |                                                                                                                                                                            |
|---------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| • | motivate our executives to manage our business to meet our short-term and long-term corporate goals and business objectives, and reward them for meeting these objectives. |

----

|         |                                                                                                                                                             |
|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------|
| • | our understanding of the amount of compensation generally paid by similarly situated companies to their executives with similar roles and responsibilities. |

----

----

|         |                                                                                                                                                                                                                                         |
|---------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| • | 50% of options with an exercise price of $2.95 vested effective June 30, 2013, and the remainder of such options will continue to vest according to the original vesting schedule (25% on each anniversary date of the original grant). |

|         |                                                                                               |
|---------|-----------------------------------------------------------------------------------------------|
| • | All options with exercise prices of $6.15 and $7.98 per share vested effective June 30, 2013. |

|         |                                                                                                                                                    |
|---------|----------------------------------------------------------------------------------------------------------------------------------------------------|
| • | Mr. Whang received accelerated vesting of 25,000, 5,000 and 27,500 options with exercise prices of $2.95, $6.15 and $7.98 per share, respectively. |

|         |                                                                                                                                                       |
|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------|
| • | Mr. Pentinga received accelerated vesting of 25,000, 2,500 and 63,750 options with exercise prices of $2.95, $6.15 and $7.98 per share, respectively. |

|         |                                                                                                                                                       |
|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------|
| • | Mr. Anderson received accelerated vesting of 20,000, 2,500 and 12,500 options with exercise prices of $2.95, $6.15 and $7.98 per share, respectively. |

|         |                                                                                                                                               |
|---------|-----------------------------------------------------------------------------------------------------------------------------------------------|
| • | Mr. Hass received accelerated vesting of 6,251, 666 and 3,750 options with exercise prices of $2.95, $6.15 and $7.98 per share, respectively. |

|         |                                                                                                                                    |
|---------|------------------------------------------------------------------------------------------------------------------------------------|
| • | Dr. Hwang received accelerated vesting of 7,500 and 3,750 options with exercise prices of $2.95 and $7.98 per share, respectively. |

----

|        |
|--------|
|        |  |
|   | RESPECTFULLY SUBMITTED, Robert F. King, ChairmanMichael GarnreiterAlfred W. GieseEgbert J.G. Goudena |

----

|                             |
|-----------------------------|
|                             |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
| Name and Principal Position | Year |   | Salary ($) |   | Bonus ($) (1) |   | Stock Awards ($) (2) |   | Option Awards ($) (2) (12) |   | Non-Equity Incentive Plan Compensation ($) (3) |   | All Other Compensation ($) | Total ($) |
| Jong S. Whang               | 2013 |   | 299,692 |  |   | — |  |   | — |  |   | 91,200 |  |   | — |  |   | 28,751 |  | (6 | ) | 419,643 |  |
| Executive Chairman          | 2012 |   | 383,077 |  |   | — |  |   | 146,297 |  |   | 181,480 |  |   | — |  |   | 36,159 |  | (7 | ) | 747,013 |  |
| and Director                | 2011 |   | 386,539 |  |   | — |  |   | 230,394 |  |   | 287,118 |  |   | 409,600 |  |   | 36,159 |  | (7 | ) | 1,349,810 |  |
| Fokko Pentinga              | 2013 |   | 300,692 |  |   | — |  |   | — |  |   | 91,200 |  |   | — |  |   | 61,301 |  | (10 | ) | 453,193 |  |
| Chief Executive             | 2012 |   | 340,613 |  |   | — |  |   | 119,700 |  |   | 420,699 |  |   | — |  |   | 80,240 |  | (10 | ) | 961,252 |  |
| Officer and Director        | 2011 |   | 309,951 |  |   | 100,000 |  |   | 201,606 |  |   | 251,222 |  |   | 257,920 |  |   | 75,895 |  | (10 | ) | 1,196,594 |  |
| Bradley C. Anderson         | 2013 |   | 215,719 |  |   | — |  |   | — |  |   | 72,960 |  |   | — |  |   | 14,435 |  | (8 | ) | 303,114 |  |
| Chief Financial             | 2012 |   | 257,291 |  |   | — |  |   | 66,497 |  |   | 82,492 |  |   | — |  |   | 18,050 |  | (8 | ) | 424,330 |  |
| Officer                     | 2011 |   | 260,315 |  |   | — |  |   | 100,794 |  |   | 125,616 |  |   | 186,560 |  |   | 17,350 |  | (8 | ) | 690,635 |  |
| Robert T. Hass              | 2013 |   | 138,615 |  |   | — |  |   | — |  |   | 22,800 |  |   | — |  |   | 10,300 |  | (9 | ) | 171,715 |  |
| Chief Accounting            | 2012 |   | 166,404 |  |   | — |  |   | 19,950 |  |   | 24,747 |  |   | — |  |   | 14,310 |  | (9 | ) | 225,411 |  |
| Officer (5)                 | 2011 |   | 165,477 |  |   | — |  |   | 11,526 |  |   | 14,352 |  |   | 65,280 |  |   | 13,853 |  | (9 | ) | 270,488 |  |
| Jeong Mo Hwang              | 2013 |   | 138,615 |  |   | — |  |   | — |  |   | 27,360 |  |   | — |  |   | 10,964 |  | (11 | ) | 176,939 |  |
| Chief Technology            | 2012 |   | 166,404 |  |   | — |  |   | 19,950 |  |   | 24,747 |  |   | — |  |   | 18,911 |  | (11 | ) | 230,012 |  |
| Officer (4)                 | 2011 |   | 69,354 |  |   | — |  |   | — |  |   | 53,834 |  |   | 29,898 |  |   | 2,692 |  | (11 | ) | 155,778 |  |

|     |                                                                                                                                                                                               |
|-----|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (1) | Represents discretionary cash bonus awarded to Mr. Pentinga on November 11, 2011 for fiscal year 2011.  No discretionary cash bonuses were awarded for fiscal years 2013 or 2012 performance. |

|     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
|-----|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (2) | Amounts represent the aggregate grant date fair value calculated in accordance with FASB ASC Topic 718. For a description of the assumptions made by the Company when calculating such grant date fair value, refer to Note 1 to the Company’s consolidated financial statements as set forth in the Company’s Form 10-K filed December 11, 2013. The number of stock awards and option awards is based upon performance in the prior fiscal year. The 2012 option awards for Mr. Pentinga include a grant of 55,000 options in recognition of his appointment to the position of Chief Executive Officer. |

|     |                                                                                                                                                                                                                                                                                                                                                                                                 |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (3) | On November 11, 2011, the Board of Directors, based upon the recommendation of the Compensation and Stock Option Committee, awarded non-equity incentive plan compensation to executives for their fiscal 2011 performance in the amounts indicated. There were no discretionary cash bonuses and no non-equity incentive plan compensation awarded for fiscal years' 2013 or 2012 performance. |

|     |                                                                                                                                                                                                                                                                                               |
|-----|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (4) | Jeong Mo Hwang was hired on April 20, 2011. All figures represent compensation from that date.  Effective June 5, 2013, the position of Chief Technology Officer was eliminated.  Dr. Hwang's compensation package and work schedule were adjusted to reflect the change in responsibilities. |

|     |                                                                                                                                                                                             |
|-----|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (5) | Effective June 5, 2013, the position of Chief Accounting Officer was eliminated.  Mr. Hass' compensation package and work schedule were adjusted to reflect the change in responsibilities. |

|     |                                                                                                                                                                                                                  |
|-----|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (6) | Amount represents car allowance of $14,192, $10,809 of life insurance premiums paid by the Company for which Mr. Whang’s spouse is the beneficiary and Company match under the 401(k) plan of $3,750. |

----

|     |                                                                                                                                                                                                                  |
|-----|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (7) | Amount represents car allowance of $18,000, $10,809 of life insurance premiums paid by the Company for which Mr. Whang’s spouse is the beneficiary and Company match under the 401(k) plan of $7,350. |

|     |                                                                                                                                                                                                                                                                                                 |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (8) | Represents Company match under the 2011, 2012 and 2013 401(k) plan of $7,350, $7,350 and $3,750, respectively, and car allowance for 2011, 2012 and 2013 of $10,000, $10,000 and $7,885, respectively.  Fiscal 2012 and 2013 amounts also include $700 and $2,800 of travel incentive payments. |

|     |                                                                                                                                                                                                                                                                                        |
|-----|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (9) | Represents Company match under the 2011, 2012 and 2013 401(k) plan of $6,853, $7,310 and $2,681, respectively, and car allowance of $7,000, $7,000 and $5,519 in fiscal years 2011, 2012 and 2013, respectively. Fiscal 2013 amount also includes $2,100 of travel incentive payments. |

|      |                                                                                                                                                                                                                                                             |
|------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (10) | Represents Company contribution under the 2011, 2012 and 2013 Netherlands pension plan of $33,090, $39,679 and $27,824, respectively, and other (primarily car allowance) of $42,804, $40,561 and $33,477 in fiscal year 2011, 2012 and 2013, respectively. |

|      |                                                                                                                                                                                                                                                                                     |
|------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (11) | Represents Company match under the 2012 and 2013 401(k) plan of $4,561 and $2,645, respectively, car allowance of $2,692, $7,000 and $5,519 for fiscal 2011, 2012 and 2013, respectively, and travel incentive payments of $7,350 and $2,800 in fiscal 2012 and 2013, respectively. |

|      |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
|------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (12) | In June 2013, the executive officers voluntarily cancelled certain outstanding stock options. Mr Whang voluntarily cancelled 30,000 options with an exercise price of $14.79 and 26,667 options with an exercise price of $17.12.  Mr. Pentinga voluntarily cancelled 3,125 options with an exercise price of $14.79 and 23,333 options with an exercise price of $17.12.  Mr. Anderson voluntarily cancelled 15,000 options with an exercise price of $14.79 and 11,667 options with an exercise price of $17.12. Mr. Hass voluntarily cancelled 5,000 options with an exercise price of $14.79 and 1,333 options with an exercise price of $17.12. Dr. Hwang voluntarily cancelled 5,000 options with an exercise price of $17.12.  Also in June 2013, the Board of Directors, based upon the recommendation of the Compensation and Stock Option Committee, accelerated the vesting of  certain outstanding option awards. |

|         |                                                                                                                                                                                                                                         |
|---------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| • | 50% of options with an exercise price of $2.95 vested effective June 30, 2013, and the remainder of such options will continue to vest according to the original vesting schedule (25% on each anniversary date of the original grant). |

|         |                                                                                               |
|---------|-----------------------------------------------------------------------------------------------|
| • | All options with exercise prices of $6.15 and $7.98 per share vested effective June 30, 2013. |

|         |                                                                                                                                                    |
|---------|----------------------------------------------------------------------------------------------------------------------------------------------------|
| • | Mr. Whang received accelerated vesting of 25,000, 5,000 and 27,500 options with exercise prices of $2.95, $6.15 and $7.98 per share, respectively. |

|         |                                                                                                                                                       |
|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------|
| • | Mr. Pentinga received accelerated vesting of 25,000, 2,500 and 63,750 options with exercise prices of $2.95, $6.15 and $7.98 per share, respectively. |

|         |                                                                                                                                                       |
|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------|
| • | Mr. Anderson received accelerated vesting of 20,000, 2,500 and 12,500 options with exercise prices of $2.95, $6.15 and $7.98 per share, respectively. |

|         |                                                                                                                                               |
|---------|-----------------------------------------------------------------------------------------------------------------------------------------------|
| • | Mr. Hass received accelerated vesting of 6,251, 666 and 3,750 options with exercise prices of $2.95, $6.15 and $7.98 per share, respectively. |

|         |                                                                                                                                    |
|---------|------------------------------------------------------------------------------------------------------------------------------------|
| • | Dr. Hwang received accelerated vesting of 7,500 and 3,750 options with exercise prices of $2.95 and $7.98 per share, respectively. |

----

|                     |
|---------------------|
|                     |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|                |   |   |   |   | Estimated Future Payouts Under Non-Equity Incentive Plan Awards |   |   |   |   |   |   |   |   |
| Name                | Grant Date (1) |   | Date Grant Approved by Board (1) |   | Threshold ($) |   | Target($) |   | Maximum ($) |   | All Other Stock Awards: Number of Shares of Stock or Units (#) (1) |   | All Other Option Awards: Number of Securities Underlying Options (#) (1) |   | Exercise or Base Price of Options Awards ($/Sh) (2) |   | Grant Date Fair Value of Stock and Option Awards ($) (3) |
| Jong S. Whang       | 12/11/2012 |   | 12/11/2012 |   | $35,840 |   | $179,200 |   | $268,800 |   | — |  |   | 50,000 |  |   | $2.95 |   | $91,200 |
| Fokko Pentinga      | 12/11/2012 |   | 12/11/2012 |   | $37,740 |   | $188,700 |   | $283,050 |   | — |  |   | 50,000 |  |   | $2.95 |   | $91,200 |
| Bradley C. Anderson | 12/11/2012 |   | 12/11/2012 |   | $19,822 |   | $99,110 |   | $148,665 |   | — |  |   | 40,000 |  |   | $2.95 |   | $72,960 |
| Robert T. Hass      | 12/11/2012 |   | 12/11/2012 |   | — |  |   | — |  |   | — |  |   | — |  |   | 12,500 |  |   | $2.95 |   | $22,800 |
| Jeong Mo Hwang      | 12/11/2012 |   | 12/11/2012 |   | — |  |   | — |  |   | — |  |   | — |  |   | 15,000 |  |   | $2.95 |   | $27,360 |

|     |                                                                                                                                                                                                                     |
|-----|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (1) | The stock and option awards listed above vest in five (5) installments; 50% on June 30, 2013 and the remaining four (4) installments in equal amounts on each of the first four anniversaries of the date of grant. |

|     |                                                                                                             |
|-----|-------------------------------------------------------------------------------------------------------------|
| (2) | The exercise price is equal to the closing price of the Company's Common Stock on the day before the grant. |

|     |                                                                                                                                                                                                   |
|-----|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (3) | See Stock-Based Compensation under Note 1 to the consolidated financial statements included in our Form 10-K filed December 11, 2013 for the assumptions used to value equity based compensation. |

----

|                     |
|---------------------|
|                     |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|                | Option Awards |   | Stock Awards |
| Name                | Number of Securities Underlying Unexercised Options (#) Exercisable |   | Number of Securities Underlying Unexercised Options (#) Unexercisable |   | Options Exercise Price ($) |   | Option Expiration Date |   | Number of Shares or Units of Stock that have Not Vested (#) |   | Market Value of Shares or Units of Stock that have Not Vested ($) |
| Jong S. Whang       | 30,000 |  |   | — |  |   | $6.90 |   | 12/8/2016 |   |   |   |   |
|                | 60,000 |  |   | — |  |   | $3.80 |   | 12/9/2018 |   |   |   |   |
|                | 20,000 |  |   | — |  |   | $6.15 |   | 11/20/2019 |   |   |   |   |
|                | 7,500 |  |   | 2,500 |  | (1) | $10.64 |   | 8/6/2020 |   |   |   |   |
|                | 36,667 |  |   | — |  |   | $7.98 |   | 12/15/2021 |   |   |   |   |
|                | 25,000 |  |   | 25,000 |  | (2) | $2.95 |   | 12/11/2022 |   |   |   |   |
|                |   |   |   |   |   |   |   |   | 24,165 |  | (3) | $176,405 |
| Fokko Pentinga      | 18,750 |  |   | — |  |   | $3.80 |   | 12/9/2018 |   |   |   |   |
|                | 10,000 |  |   | — |  |   | $6.15 |   | 11/20/2019 |   |   |   |   |
|                | 5,001 |  |   | 1,666 |  | (1) | $10.64 |   | 8/6/2020 |   |   |   |   |
|                | 85,000 |  |   | — |  |   | $7.98 |   | 12/15/2021 |   |   |   |   |
|                | 25,000 |  |   | 25,000 |  | (2) | $2.95 |   | 12/11/2022 |   |   |   |   |
|                |   |   |   |   |   |   |   |   | 19,166 |  | (4) | $139,912 |
| Bradley C. Anderson | 10,000 |  |   | — |  |   | $8.51 |   | 4/24/2016 |   |   |   |   |
|                | 5,000 |  |   | — |  |   | $6.90 |   | 12/8/2016 |   |   |   |   |
|                | 15,000 |  |   | — |  |   | $7.30 |   | 2/19/2017 |   |   |   |   |
|                | 15,000 |  |   | — |  |   | $3.80 |   | 12/9/2018 |   |   |   |   |
|                | 7,500 |  |   | — |  |   | $6.15 |   | 11/20/2019 |   |   |   |   |
|                | 3,750 |  |   | 1,250 |  | (1) | $10.64 |   | 8/6/2020 |   |   |   |   |
|                | 16,667 |  |   | — |  |   | $7.98 |   | 12/15/2021 |   |   |   |   |
|                | 20,000 |  |   | 20,000 |  | (2) | $2.95 |   | 12/11/2022 |   |   |   |   |
|                |   |   |   |   |   |   |   |   | 11,040 |  | (5) | $80,592 |
| Robert T. Hass      | 5,000 |  |   | — |  |   | $6.90 |   | 12/8/2016 |   |   |   |   |
|                | 9,000 |  |   | — |  |   | $3.80 |   | 12/9/2018 |   |   |   |   |
|                | 2,667 |  |   | — |  |   | $6.15 |   | 11/20/2019 |   |   |   |   |
|                | 1,000 |  |   | 333 |  | (1) | $10.64 |   | 8/6/2020 |   |   |   |   |
|                | 5,000 |  |   | — |  |   | $7.98 |   | 12/15/2021 |   |   |   |   |
|                | 6,250 |  |   | 6,250 |  | (2) | $2.95 |   | 12/1/2022 |   |   |   |   |
|                |   |   |   |   |   |   |   |   |   |   |   |
|                |   |   |   |   |   |   |   |   | 2,707 |  | (6) | $19,761 |
| Jeong Mo Hwang      | 4,020 |  |   | — |  |   | $5.01 |   | 6/25/2019 |   |   |   |   |
|                | 5,000 |  |   | — |  |   | $6.15 |   | 11/20/2019 |   |   |   |   |
|                | 5,000 |  |   | — |  |   | $7.98 |   | 12/15/2021 |   |   |   |   |
|                | 7,500 |  |   | 7,500 |  | (2) | $2.95 |   | 12/11/2022 |   |   |   |   |
|                |   |   |   |   |   |   |   |   | 1,875 |  | (7) | $13,688 |

|     |                                                     |
|-----|-----------------------------------------------------|
| (1) | Unvested option awards will vest on August 6, 2014. |

|     |                                                                                                                                       |
|-----|---------------------------------------------------------------------------------------------------------------------------------------|
| (2) | Unvested option awards will vest in equal installments on the first through fourth anniversaries of the December 11, 2012 grant date. |

|     |                                                                                                                                                                                                             |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (3) | Mr. Whang's restricted stock awards will vest as follows - 5,833 in November 2013; 4,583 in December 2013; 1,250 in August 2014; 3,333 in November 2014; 4,583 in December 2014 and 4,583 in December 2015. |

----

|     |                                                                                                                                                                                                              |
|-----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (4) | Mr. Pentinga's restricted stock awards will vest as follows - 4,167 in November 2013; 3,750 in December 2013; 833 in August 2014; 2,916 in November 2014; 3,750 in December 2014 and 3,750 in December 2015. |

|     |                                                                                                                                                                                                              |
|-----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (5) | Mr. Anderson's restricted stock awards will vest as follows - 2,708 in November 2013; 2,083 in December 2013; 625 in August 2014; 1,458 in November 2014; 2,083 in December 2014 and 2,083 in December 2015. |

|     |                                                                                                                                                                                               |
|-----|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (6) | Mr. Hass' restricted stock awards will vest as follows - 499 in November 2013; 625 in December 2013; 167 in August 2014; 166 in November 2014; 625 in December 2014 and 625 in December 2015. |

|     |                                                                                                                                        |
|-----|----------------------------------------------------------------------------------------------------------------------------------------|
| (7) | Dr. Hwang's restricted stock awards will vest equally on the second, third and fourth anniversary of the December 15, 2011 grant date. |

|                     |
|---------------------|
|                     |  |  |  |  |  |  |  |  |  |  |  |  |
|                |   | Option Awards |   | Stock Awards |
| Name                |   | Number of Shares Acquired on Exercise (#) |   | Value Realized on Exercise ($)(1) |   | Number of Shares Acquired on Vesting (#) |   | Value Realized on Vesting ($)(2) |
| Jong S. Whang       |   | — |  |   | — |  |   | 24,167 |  |   | 75,551 |  |
| Fokko Pentinga      |   | — |  |   | — |  |   | 10,625 |  |   | 34,616 |  |
| Bradley C. Anderson |   | — |  |   | — |  |   | 7,917 |  |   | 25,638 |  |
| Robert T. Hass      |   | — |  |   | — |  |   | 3,292 |  |   | 10,234 |  |
| Jeong Mo Hwang      |   | — |  |   | — |  |   | 625 |  |   | 1,875 |  |

|     |                                                                                                                                                                                                                                  |
|-----|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (1) |  The value realized equals the difference between the option exercise price and the fair market value of Amtech common stock on the date of exercise, multiplied by the number of shares for which the option was exercised. |

|     |                                                                                                                                             |
|-----|---------------------------------------------------------------------------------------------------------------------------------------------|
| (2) | The value realized equals the fair market value of Amtech common stock on the vesting date, multiplied by the number of shares that vested. |

----

|                         |
|-------------------------|
|                         |  |  |  |  |  |  |  |  |  |  |  |
| Name                    | Fees Earned or Paid in Cash ($) |   | Option Awards ($) (1) |   | All other Comp. ($) |   | Total ($) |
|                    |   |   |   |   |   |   |   |
| Jong S. Whang (2)       | — |  |   | — |  |   | — |  |   | — |  |
| Fokko Pentinga (2)      | — |  |   | — |  |   | — |  |   | — |  |
| Michael Garnreiter (3)  | 42,450 |  |   | 10,944 |  |   | — |  |   | 53,394 |  |
| Alfred W. Giese (3)     | 38,675 |  |   | 10,944 |  |   | — |  |   | 49,619 |  |
| Egbert J.G. Goudena (3) | 23,925 |  |   | 10,944 |  |   | — |  |   | 34,869 |  |
| Robert F. King (3)      | 40,150 |  |   | 10,944 |  |   | — |  |   | 51,094 |  |

|     |                                                                                                                                                                                                                                                                                                                                                             |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (1) | Amounts represent the aggregate grant date fair value computed in accordance with FASB ASC Topic 718. For a description of the assumptions made by the Company when calculating such grant date fair value, refer to Note 1 to the Company’s consolidated financial statements as set forth in the Company’s Form 10-K filed December 11, 2013. |

|     |                                                                                                                   |
|-----|-------------------------------------------------------------------------------------------------------------------|
| (2) | Directors who are full-time employees of our Company receive no additional compensation for serving as directors. |

|     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|-----|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (3) | In June 2013, these directors received accelerated vesting of certain stock options.  50% of options with an exercise price of $2.95 vested effective June 30, 2013, and the remainder of such options will continue to vest according to the original vesting schedule (one-third on each anniversary date of the original grant). All options with exercise prices of  $7.98 per share vested effective June 30, 2013. In fiscal 2013, each of these directors received accelerated vesting of 3,000 stock options with an exercise price of $2.95 per share and 4,000 stock options with an exercise price of $7.98 per share. |

----

|                                                          |
|----------------------------------------------------------|
|                                                          |  |  |  |  |  |  |  |  |
|                                                     | Number of securities to beissued upon exercise ofoutstanding options,warrants and rights(a) |   | Weighted-averageexercise price ofoutstanding options,warrants and rights (b) |   | Number of securitiesremaining available forfuture issuance underequity compensation plans(excluding securitiesreflected in column (a))(c) |
| Plan Category                                            |   |  |   |   |  |   |   |  |
| Equity compensationplans approved bysecurity holders (1) | 1,059,567 |  |   | 6.71 |  |   | 259,742 |  |
| Equity compensationplans not approved bysecurity holders | — |  |   |   |  |   | — |  |
| Total                                                    | 1,059,567 |  |   |   |  |   | 259,742 |  |

|     |                                                                                                                                                                               |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (1) | Represents the 1998 Employee Stock Option Plan, the 2007 Employee Stock Incentive Plan and the Non-Employee Director Stock Option Plan and any respective amendments thereto. |

|                                       |
|---------------------------------------|
|                                       |  |  |  |  |  |  |  |
| Name and Address (1) (2)              |   | No. of Shares of Common Stock Beneficially Held (3) |   | Percent of Common Stock Ownership (3) |
| Officers and Directors:               |   |   |   |   |
| Jong S. Whang                         |   | 301,863 |  | (4 | ) | 3.1 | % |
| Fokko Pentinga                        |   | 193,751 |  | (5 | ) | 2.0 | % |
| Bradley C. Anderson                   |   | 149,308 |  | (6 | ) | 1.5 | % |
| Michael Garnreiter                    |   | 31,000 |  | (7 | ) | * |  |
| Alfred W. Giese                       |   | 27,353 |  | (8 | ) | * |  |
| Egbert J. G. Goudena                  |   | 28,000 |  | (9 | ) | * |  |
| Robert F. King                        |   | 45,000 |  | (10 | ) | * |  |
| Director and Officer Total (9 people) |   | 776,275 |  | (11 | ) | 8.1 | % |

----

|     |                                                                                                                            |
|-----|----------------------------------------------------------------------------------------------------------------------------|
| (1) | The address for each person listed in this table is c/o Amtech Systems, Inc., 131 South Clark Drive, Tempe, Arizona 85281. |

|     |                                                                                                                                                                                                                                                                                                          |
|-----|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (2) | Mr. Whang is our Executive Chairman and Chairman of the Board of Directors. Mr. Pentinga is our President and CEO and is a director. Mr. Anderson is our Executive Vice President-Chief Financial Officer, Treasurer and Secretary. Messrs. Garnreiter, Giese, Goudena and King are directors of Amtech. |

|     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (3) | Based on 9,583,867 shares of common stock outstanding as of January 6, 2014. The share amounts and percentages shown include shares of common stock actually owned as of January 6, 2014, and shares of common stock with respect to which the person had the right to acquire beneficial ownership within 60 days of such date pursuant to options or warrants. All shares of common stock that the identified person had the right to acquire within 60 days of January 6, 2014, upon the exercise of options or warrants, are deemed to be outstanding when computing the percentage of the securities owned by such person, but are not deemed to be outstanding when computing the percentage of the securities owned by any other person. |

|     |                                                                                                          |
|-----|----------------------------------------------------------------------------------------------------------|
| (4) | Includes 208,333 shares issuable upon exercise of options exercisable within 60 days of January 6, 2014. |

|     |                                                                                                          |
|-----|----------------------------------------------------------------------------------------------------------|
| (5) | Includes 166,251 shares issuable upon exercise of options exercisable within 60 days of January 6, 2014. |

|     |                                                                                                          |
|-----|----------------------------------------------------------------------------------------------------------|
| (6) | Includes 109,792 shares issuable upon exercise of options exercisable within 60 days of January 6, 2014. |

|     |                                                                                                         |
|-----|---------------------------------------------------------------------------------------------------------|
| (7) | Includes 31,000 shares issuable upon exercise of options exercisable within 60 days of January 6, 2014. |

|     |                                                                                                         |
|-----|---------------------------------------------------------------------------------------------------------|
| (8) | Includes 25,833 shares issuable upon exercise of options exercisable within 60 days of January 6, 2014. |

|     |                                                                                                         |
|-----|---------------------------------------------------------------------------------------------------------|
| (9) | Includes 21,000 shares issuable upon exercise of options exercisable within 60 days of January 6, 2014. |

|      |                                                                                                         |
|------|---------------------------------------------------------------------------------------------------------|
| (10) | Includes 35,000 shares issuable upon exercise of options exercisable within 60 days of January 6, 2014. |

|      |                                                                                                          |
|------|----------------------------------------------------------------------------------------------------------|
| (11) | Includes 581,208 shares issuable upon exercise of options exercisable within 60 days of January 6, 2014. |

|                                                                     |
|---------------------------------------------------------------------|
|                                                                     |  |  |  |  |  |  |
| Name and Address                                                    |   | No. of Shares of Common Stock Beneficially Held (1) |   | Percent of Common Stock Ownership (1) |
| 5% Shareholders                                                     |   |   |   |   |
| Leslie J. Schreyer, as Trustee FBO the issue of Jonathan D. Sackler |   | 791,750 |  | (2) | 8.3 | % |

|     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (1) | Based on 9,583,867 shares of common stock outstanding as of January 6, 2014. The share amounts and percentages shown include shares of common stock actually owned as of January 6, 2014, and shares of common stock with respect to which the person had the right to acquire beneficial ownership within 60 days of such date pursuant to options or warrants. All shares of common stock that the identified person had the right to acquire within 60 days of January 6, 2014, upon the exercise of options or warrants, are deemed to be outstanding when computing the percentage of the securities owned by such person, but are not deemed to be outstanding when computing the percentage of the securities owned by any other person. |

|     |                                                                                                                                                                                                                                                                                             |
|-----|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (2) | Leslie J. Schreyer is Trustee under a Trust Agreement dated December 23, 1989 FBO the issue of Jonathan D. Sackler. Represents shares held in the Trust, for which Leslie J. Schreyer serves as sole Trustee. Leslie J. Schreyer has no pecuniary interest in the shares held by the Trust. |

----

|                                          |
|------------------------------------------|
|                                          |  |  |  |  |  |  |  |
|                                     | Year Ended |   | Year Ended |
|                                     | Sept. 30, 2013 |   | Sept. 30, 2012 |
| Audit Fees (1)                           | $ | 392,153 |  |   | $ | 441,011 |  |
| Audit-Related Fees (2)                   | 29,977 |  |   | 17,771 |  |
| Tax Fees                                 | — |  |   | — |  |
| All Other Fees                           | — |  |   | — |  |
|      Total Fees | $ | 422,130 |  |   | $ | 458,782 |  |

|     |                                                                                                                                                                                                                                                                                                               |
|-----|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (1) | Annual audit and  review of financial statements included in the Company’s reports on Form 10-Q and Form 10-K, including an audit of the Company’s internal control over financial reporting, and services normally provided by the auditors in connection with statutory and regulatory filings. |

|     |                                                                                                             |
|-----|-------------------------------------------------------------------------------------------------------------|
| (2) | Consists primarily of assurance services related to the legal restructure of operations in The Netherlands. |

----

|            |
|------------|
|            |  |
| EXHIBITNO. | DESCRIPTION |
| 31.1       | Certification Pursuant to Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as Amended. Filed herewith. |
| 31.2       | Certification Pursuant to Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as Amended. Filed herewith. |

----

|                        |
|------------------------|
|                        |  |  |  |  |
| SIGNATURE              |   | TITLE |   | DATE |
|                   |   |   |   |   |
| /s/Jong S. Whang       |   | Executive Chairman and |   | January 24, 2014 |
| Jong S. Whang          |   | Chairman of the Board |   |   |
|                   |   |   |   |   |
| /s/Fokko Pentinga      |   | Chief Executive Officer |   | January 24, 2014 |
| Fokko Pentinga         |   | and President |   |   |
|                   |   | (Principal Executive Officer) |   |   |
|                   |   |   |   |   |
| /s/Bradley C. Anderson |   | Executive Vice President – Finance and Chief Financial Officer |   | January 24, 2014 |
| Bradley C. Anderson    |   | (Principal Financial and Accounting Officer) |   |   |
|                   |   |   |   |   |
| /s/Michael Garnreiter  |   | Director |   | January 24, 2014 |
| Michael Garnreiter     |   |   |   |   |
|                   |   |   |   |   |
| /s/Alfred W. Giese     |   | Director |   | January 24, 2014 |
| Alfred W. Giese        |   |   |   |   |
|                   |   |   |   |   |
| /s/Egbert J.G. Goudena |   | Director |   | January 24, 2014 |
| Egbert J.G. Goudena    |   |   |   |   |
|                   |   |   |   |   |
| /s/Robert F. King      |   | Director |   | January 24, 2014 |
| Robert F. King         |   |   |   |   |
|                   |   |   |   |   |
|                   |
|                   |   |   |   |   |
|                   |   |   |   |   |
|                   |   |   |   |   |
|                   |   |   |   |   |
|                   |   |   |   |   |
|                   |   |   |   |   |