UNITED STATES SECURITIES AND EXCHANGE COMMISSION




WASHINGTON, D.C. 20549




FORM 10-K/A Amendment No. 1







|[X] |  | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended: September 30, 2005
|--- |  | ----------------------------------------------------------------------------------------------------------------------------------



OR


|[  ] |  | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
SECURITIES EXCHANGE ACT OF 1934For the transition period from __________ to __________
|---- |  | -----------------------------------------------------------------------------------------------------------------------------------------------



Commission File Number: 0-11412




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







|Arizona                                                        |  |  |  | 86-0411215                          
|-------------------------------------------------------------- |  |  |  | ------------------------------------
|(State or other
jurisdiction of incorporation or organization) |  |  |  | (I.R.S. Employer Identification 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: Common Stock, $.01 Par Value (Title of
Class)




Indicate by
check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing
requirements for the past 90 days. Yes [X]  No [  ]




Indicate by check mark if
disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of
registrants knowledge in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to
this Form 10-K. [  ]




Indicate by check mark whether
the registrant is an accelerated filer (as defined in Exchange Act Rule 12(b)(2). Yes [  ]  No [X]







---





EXPLANATORY NOTE




This is Amendment No. 1 to the
Registrants annual report on Form 10-K for the year ended September 30, 2005, which was originally filed with the Securities and Exchange
Commission on December 29, 2005. This amendment is being filed to include responses to the items required by Part III, which originally were expected
to be incorporated by reference to the Registrants definitive Proxy Statement to be delivered to its shareholders in connection with its 2006
Annual Meeting of Shareholders. This amendment is also being filed to update the exhibits by adding those exhibits listed in Item 15 of Part IV
herein.




TABLE OF CONTENTS


|           |  |  |  |                                                                                                |  | Page
|---------- |  |  |  | ---------------------------------------------------------------------------------------------- |  | ----
|           |  |  |  | PART III                                                                                       |  |     
|Item
10    |  |  |  | Directors and Executive Officers of the Registrant                                             |  |     
|Item
11.   |  |  |  | Executive Compensation                                                                         |  |     
|Item
12.   |  |  |  | Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters |  |     
|Item
13.   |  |  |  | Certain Relationships and Related Transactions                                                 |  |     
|Item
14.   |  |  |  | Principal Accountant Fees and Services                                                         |  |     
|           |  |  |  | PART IV                                                                                        |  |     
|Item
15.   |  |  |  | Exhibits and Financial Statement Schedules                                                     |  |     
|Signatures |  |  |  |                                                                                                |  |     

---





PART III


|ITEM
10. |  | DIRECTORS AND EXECUTIVE OFFICERS OF THE
REGISTRANT
|-------- |  | --------------------------------------------------



(1) The following table sets
forth information regarding the officers and directors of the Company. The subsequent paragraphs contain biographical data for each
director.







|Name                  |  |  |  | Age |  | Position with the Company                                                           
|--------------------- |  |  |  | --- |  | ------------------------------------------------------------------------------------
|Jong S.
Whang         |  |  |  | 60  |  | President, Chief Executive Officer and Director                                     
|Robert T.
Hass        |  |  |  | 55  |  | Vice
President  Finance, Chief Financial Officer, Treasurer, Secretary and Director
|Lawrence D.
Firestone |  |  |  | 47  |  | Director                                                                            
|Robert F.
King        |  |  |  | 72  |  | Director                                                                            
|Robert
Averick        |  |  |  | 39  |  | Director                                                                            



Jong S.
Whang has been President, Chief Executive Officer and a Director of the Company since its inception in 1981, and was one of its founders. Mr.
Whangs responsibilities as President include the sales effort for the Companys semiconductor equipment business and the development of new
products and business opportunities in that industry. He has 32 years of experience in the semiconductor industry, including time spent in both
processing and manufacturing of equipment components and systems. From 1973 until 1979, he was employed by Siltronics, Inc., initially as a technician
working with chemical vapor deposition, and later as manager of the quartz fabrication plant with responsibility of providing technical marketing
support. From 1979 until 1981, he was employed by U.S. Quartz, Inc. as manufacturing manager. In 1981, he left U.S. Quartz to form the
Company.




Robert T. Hass has been
Vice President  Finance, Chief Financial Officer, Treasurer and Secretary of the Company since June 1992, and a Director of the Company since
February 1996. From 1991 until May 1992, he operated a financial consulting practice. From 1985 to 1991, Mr. Hass was Director of Accounting Services
and then Controller for Lifeshares Group, Inc., and from 1988 to 1991 was Controller and Chief Accounting Officer of some of Lifeshares
subsidiaries. From 1984 to 1985, he was Vice President  Finance and Treasurer of The Victorio Company. From 1977 to 1984, he served in various
capacities including Vice President, Chief Financial Officer and Treasurer of Altamil Corporation, then a public diversified manufacturing company.
From 1972 to 1977, he was an auditor with Ernst & Ernst, now known as Ernst & Young. He is a Certified Public Accountant.




Lawrence D. Firestone has
been a director of the Company since October 27, 2005. Mr. Firestone is, and has been since 1999, the Chief Financial Officer, Secretary and Treasurer
of Applied Films Corporation (Nasdaq: AFCO), a supplier of thin film deposition equipment to several industries, including the solar cell industry,
with global operations, and the Senior Vice President of Applied Films since July 2003. From 1996 until 1999, Mr. Firestone served as Vice President
and Chief Operating Officer of Avalanche Industries, Inc., a contract manufacturer of custom cables and harnesses. From 1993 to 1996, Mr. Firestone
served as Director of Finance and Operations for the Woolson Spice and Coffee Company, a gourmet coffee roasting and distribution company, and from
1988 to 1993, as Vice President and Chief Financial Officer for TechniStar Corporation, a manufacturer of robotic automation equipment. From 1981 to
1988, Mr. Firestone served in various capacities and finally as Vice President and Chief Financial Officer at Colorado Manufacturing Technology, a
contract manufacturer that specialized in printed circuit board and cable assembly. Additionally, until July 2005, Mr. Firestone served on the board of
directors of HyperSpace Communications, Inc. (AMEX: HCO), and he served as chairman of their audit and governance committees. Mr. Firestone has a
Bachelor of Science degree in business administration with a concentration in accounting from Slippery Rock State College.




Robert F. King has been a
Director of the Company since May 2003. Since 1989, Mr. King has been President of King Associates, which provides consulting services to equipment
companies serving the semiconductor and flat panel display industries. He currently serves on the advisory board of a privately-held company, which
provides equipment to the flat panel display industry. From 1968 to 1988, Mr. King was employed at Varian Associates, where he served in various
marketing positions, including Vice President of Marketing for the Semiconductor Equipment Division. Mr. King also served on the Board of Directors of
Varians joint venture semiconductor equipment companies located in Korea and Japan.




2


---



Robert M. Averick has been
the Preferred Stock Director since July 8, 2005. Mr. Averick is currently a Vice President, Portfolio Manager at Richard L. Scott Investments, LLC
(RLSI), a family investment office located in Stamford, Connecticut. Mr. Averick co-manages a public equity portfolio on behalf of RLSI
where he is responsible for all aspects of the investment decision-making process. Prior to joining RLSI in 2000, Mr. Averick was a Senior Associate
with Prudential Investments Structured Finance Group where he focused on highly structured, private and 144A asset-backed transactions. Mr. Averick has
additional work experience in Strategic Planning and Consulting. Mr. Averick received an undergraduate degree in Economics from The University of
Virginia and a Masters in Business Administration in Finance and Entrepreneurial Management from The University of Pennsylvania, The Wharton School of
Business.




Audit Committee and Audit Committee Financial
Expert




The Company has a
separately-designated standing audit committee established in accordance with section 3(a)(58)(A) of the Securities Exchange Act of 1934, as amended.
The Companys Audit Committee is comprised as follows: Robert M. Averick, Lawrence D. Firestone and Robert F. King.




The Board of Directors annually
reviews the independence of the Companys Audit Committee members in view of the NASDs listing standards and the Securities and
Exchange Commissions (SEC) definitions of independence for audit committee members. The Board has determined that each of the three
members of the Audit Committee meets those definitions and standards. Additionally, each member of the Audit Committee is financially literate, and one
of the Audit Committee members, Lawrence D. Firestone, has financial management expertise as required by Nasdaqs rules and meets the SECs
definition of an audit committee financial expert.




Section 16(a) Beneficial Ownership Reporting
Compliance




Section 16(a) of the Securities
Exchange Act of 1934, as amended, requires the Companys directors and executive officers, as well as persons beneficially owning more than 10% of
our outstanding Common Stock, to file certain reports of ownership with the SEC within specified time periods. Such officers, directors and
shareholders are also required by SEC rules to furnish the Company with copies of all Section 16(a) forms they file.




Based solely on our review of
such forms received by us during the fiscal year ended September 30, 2005, or written representations from certain reporting persons, we believe that
between October 1, 2004 and September 30, 2005, all Section 16(a) filing requirements applicable to its officers, directors and 10% shareholders were
complied with, except that: (i) Mr. King failed to timely make such required filings with respect to an automatic option grant on July 8, 2005; and
(ii) Mr. Averick failed to timely make such required filings with respect to his election as a director of the Company on July 8, 2005 and with respect
to an automatic option grant on the same date. In addition, no filing under Section 16(a) has been made with respect to the beneficial ownership of
Common Stock by Richard L. Scott.




CODE OF ETHICS




The Board of Directors has
adopted a Code of Ethics for all employees of the Company, as recommended by the Audit Committee. A copy of this Code of Ethics may be viewed on our
website (www.amtechsystems.com), or obtained at no charge by written request to the Companys Corporate Secretary.




3


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|ITEM
11. |  | EXECUTIVE COMPENSATION
|-------- |  | ----------------------



The following table sets forth
information regarding annual and long-term compensation for services rendered to the Company during the fiscal years ended September 30, 2005, 2004 and
2003 by the Companys Chief Executive Officer and the other most highly compensated executive officer of the Company who received annual
compensation exceeding $100,000 during such periods (collectively, the Named Executive Officers).




SUMMARY COMPENSATION TABLE







|                    |  |  |      |  |  |   |         |  |  | Long-Term Compensation |       
|------------------- |  |  | ---- |  |  | - | ------- |  |  | ---------------------- | ------
|
|
|Jong S.
Whang       |  |  | 2005 |  |  | $ | 150,722 |  |  | $                      | 18,555
|President and
Chief |  |  | 2004 |  |  |   | 150,722 |  |  |                        |      
|Executive
Officer   |  |  | 2003 |  |  |   | 150,722 |  |  |                        |      
|                   
|Robert T.
Hass      |  |  | 2005 |  |  | $ | 102,000 |  |  | $                      |      
|Vice
President     |  |  | 2004 |  |  |   | 102,000 |  |  |                        | 57,461
|Finance             |  |  | 2003 |  |  |   | 102,000 |  |  |                        |      






|(1) |  | Neither Mr. Whang nor Mr. Hass received personal benefit
perquisites in excess of the lesser of $50,000 or 10% of their aggregate salary and bonus.
|--- |  | ---------------------------------------------------------------------------------------------------------------------------------------------------

|(2) |  | Effective March 15, 2001, Mr. Whang entered into a five-year
employment agreement with the Company. The agreement specifies an annual base salary of $188,402, with annual increases of no less than 5%. Effective
April 1, 2001, Mr. Whang voluntarily reduced his annual salary by 20% to $150,722 and Mr. Hass voluntarily reduced his annual salary by 15% to
$102,000, which reductions remained in effect as of the end of fiscal 2005. Mr. Hass annual salary was restored to $120,000 effective December
2005.
|--- |  | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|(3) |  | See Employment And Change In Control Arrangements
for a description of how Mr. Whangs incentive compensation is determined.
|--- |  | ------------------------------------------------------------------------------------------------------------------------------

|(4) |  | The discretionary cash bonus granted to Mr. Hass in 2004 was in
consideration for work performed in connection with the acquisition of Bruce Technologies, Inc.
|--- |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------



Option Grants in Last Fiscal Year




There were no stock option grants
during the 2005 fiscal year to any of the Named Executive Officers.




4


---



Aggregated Option Exercises and Fiscal Year-End Option
Values




The following table sets forth
information (on an aggregated basis) concerning exercises of stock options during the 2005 fiscal year by each of the Named Executive Officers, and the
year-end value of unexercised options.







|               |  |  |   |  |  | Number of Securities Underlying Unexercised Options
at Fiscal Year-End (#) |   | Value of Unexercised In-The-Money
Options at Fiscal Year-End ($) (1) | 
|-------------- |  |  | - |  |  | -------------------------------------------------------------------------- | - | ---------------------------------------------------------------------- | 
|
|Jong S.
Whang  |  |  |  |  |  |                                                                            |  |                                                                        | 
|Robert T.
Hass |  |  |  |  |  |                                                                            |  |                                                                        | 






|(1) |  | Options are in-the-money at the fiscal year-end if
the fair market value ($5.75 per share, based on the closing price of the Companys Common Stock on the Nasdaq Stock Market on September 30, 2005)
of the underlying securities exceeds the exercise or base price of the option on such date. The dollar values in the last two columns of the table are
the amounts by which the sum of the fair market values of the in-the-money options exceeds the sum of their exercise prices.
|--- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



EMPLOYMENT AND CHANGE IN CONTROL
ARRANGEMENTS




On March 15, 2001, the Company
entered into a five-year employment agreement with its President, Jong S. Whang. Under the terms of the agreement, Mr. Whang is entitled to an annual
base salary of $188,402, and annual base salary increases of at least 5% to be determined by our Board of Directors. Mr. Whang is also entitled to
receive annual incentive cash compensation of up to the lesser of 50% of his base salary or 10% of the Companys earnings before taxes and
extraordinary items (after deducting the sum of such bonuses), based on the follow criteria: (i) a bonus equal to 2% of the annual earnings of the
Company before taxes and extraordinary items and (ii) a bonus equal to 2% of the amount by which the revenues of the Company for the applicable fiscal
year exceeds such revenues for the previous fiscal year. In addition, Mr. Whang was granted an option to purchase 150,000 shares of Common Stock
pursuant to the terms of his employment agreement. These options were granted on March 15, 2001, and vest at the rate of 20% per full year of service
over a five-year period. To the extent not already exercisable, the options become immediately exercisable upon: (i) the dissolution or liquidation of
the Company, or a reorganization, merger or consolidation in which all, or substantially all, prior shareholders do not continue to own more than 60%
of the then outstanding shares of Common Stock and voting securities, (ii) the sale of all, or substantially all, of the assets of the Company or (iii)
the occurrence of a change in control of the Company, as discussed in the agreement. The agreement also contains confidentiality and non-compete
provisions with which Mr. Whang must comply. Mr. Whang is also entitled to participate in any benefit plans generally available to employees of the
Company. Finally, the Company is required to purchase a $250,000 life insurance policy on the life of Mr. Whang, with his spouse as the beneficiary of
such policy. To date, Mr. Whang has waived the Companys compliance with the latter requirement.




Under the terms of Mr.
Whangs employment agreement, if he is terminated other than for cause, or he terminates his employment for good reason
(as such terms are defined in his employment agreement), he is entitled to receive, as severance pay, salary, incentive compensation and vacation
accrued through the date of termination plus the following: (i) an amount equal to two years of Mr. Whangs base salary in effect on the
termination date; (ii) a pro-rated portion of the amount of incentive compensation Mr. Whang would earn for the fiscal year in which the termination
occurs if the results of operations of the Company for the period from the beginning of such fiscal year to the termination date were annualized; (iii)
full vesting of all stock options issued under the employment agreement; and (iv) vesting of a pro-rated portion of the number of stock options that
would have vested for the fiscal year in which the termination occurs.




Mr. Whangs employment
agreement also provides for benefits should his employment with the Company be terminated following a change in control. If Mr. Whangs employment
with the Company is terminated within one year following the occurrence of a change of control, either by the Company for any reason other than for
cause, or by Mr. Whang for good reason, the Company would be required to pay him a lump sum payment equal to three years of his annual base salary in
effect on the termination date and the maximum amount of incentive compensation that he could earn for the fiscal year in which the termination date
occurs. In addition, all unvested stock options held by him would vest immediately.




5


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The Company has also entered into
a severance agreement with Robert T. Hass, its Vice President  Finance, which provides for severance benefits similar to those described above
for Mr. Whang, with the exception that Mr. Hass is entitled to a lump sum severance payment equal to one years base salary should his employment
be terminated within one year following a change in control.




Directors Compensation




Directors who are full-time
employees of the Company receive no additional compensation for serving as directors. Non-employee directors receive an annual retainer of $6,000 and
fees of $1,000 per Board meeting attended in person and $500 per Board meeting attended telephonically and per committee meeting attended. In addition,
under the Companys Non-Employee Directors Stock Option Plan, each outside director currently receives an annual grant of options to purchase
6,000 shares of Common Stock, or such other number of shares as maybe determined by the Board, when first elected or appointed to the Board, and 5,000
shares of Common Stock, or such other number of shares as maybe determined by the Board, upon each re-election to the Board at the Companys
Annual Meeting of Shareholders. The exercise price of the options is set at the fair market value of Common Stock on the date of grant. Each option has
a term of ten years and is exercisable in three equal installments commencing on the first anniversary of the date of grant and continuing for the two
successive anniversaries thereafter. In the event of disability (as defined in the plan) or death of an outside director, all options remain
exercisable for a period of 30 days following the date such person ceased to be a director, or such other date as may be determined by the Board, but
only to the extent such options were exercisable on the date the director ceased to be a director. Furthermore, the director serving as the Chairman of
the Audit Committee and the Audit Committee Financial Expert receives an annual retainer of $14,000.




Compensation Committee Interlocks and Insider
Participation




The Compensation and Option
Committee is presently comprised of Messrs. Robert M. Averick and Robert F. King, who are not, and have never been, officers or employees of the
Company.


|ITEM
12. |  | SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT
AND RELATED STOCKHOLDER MATTERS
|-------- |  | ----------------------------------------------------------------------------------------------



SECURITIES AUTHORIZED FOR ISSUANCE UNDER EQUITY COMPENSATION
PLANS




The following table sets forth
certain information, as of September 30, 2005, concerning outstanding options and rights to purchase Common Stock granted to participants in all of the
Companys equity compensation plans and the number of shares of Common Stock remaining available for issuance under such equity compensation
plans.


|                                                               |  |  |  | Number of securities to be issued upon exercise
of outstanding options, warrants and rights (a) |         | Weighted-average exercise price of
outstanding options, warrants and rights (b) |  | Number of securities remaining available for
future issuance under equity compensation plans (excluding securities reflected in column (a)) (c)
|-------------------------------------------------------------- |  |  |  | ----------------------------------------------------------------------------------------------- | ------- | ------------------------------------------------------------------------------- |  | -----------------------------------------------------------------------------------------------------------------------------------------------
|Plan
Category                                                  |  |  |  |                                                                                                 |         |                                                                                 |  |                                                                                                                                                
|Equity
compensation plans approved by security holders (1)     |  |  |  |                                                                                                 | 458,206 |                                                                                 |  |                                                                                                                                                
|Equity
compensation plans not approved by security holders (2) |  |  |  |                                                                                                 | 70,000  |                                                                                 |  |                                                                                                                                                
|Total                                                          |  |  |  |                                                                                                 | 528,206 |                                                                                 |  |                                                                                                                                                






|(1) |  | Represents the 1995 and 1998 Employee Stock Option Plans and the
Non-Employee Director Stock Option Plan and any respective amendments thereto.
|--- |  | -----------------------------------------------------------------------------------------------------------------------------------------------

|(2) |  | Represents (i) 10,000 shares of common stock issuable upon
exercise of options granted to non-employee directors under stock purchase agreements prior to the 1996 establishment of the Non-Employee Director
Stock
|--- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



6


---

| |  | Option Plan, with an exercise price of $1.26; and (ii) 60,000
shares of common stock issuable upon exercise of a warrant issued to the placement agent in connection with the private placement in April 2005, having
an exercise price of $4.67. The options and warrants under these plans are fully vested.
| |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



SECURITY OWNERSHIP OF CERTAIN BENEFICIAL
OWNERS




The following table sets forth
certain information concerning the beneficial ownership of our Common Stock and Preferred Stock as of January 20, 2006 by (i) each director and
executive officer of the Company, including the Named Executive Officers, (ii) all executive officers and directors of the Company as a group and (iii)
each person known by the Company to be the beneficial owner of more than 5% of our Common Stock. This information was determined in accordance with
Rule 13d-3 under the Securities Exchange Act of 1934, as amended, and is based upon the information furnished by the persons listed below. Except as
otherwise indicated, each shareholder listed possesses sole voting and investment power with respect to the shares indicated as being beneficially
owned.







|Name and Address (1)(2)                                                |  |  |  | No. of Shares of Common Stock Beneficially Held
(3) |         | Percent of Common Stock Ownership (3) |  | No. of Shares of Preferred Stock Beneficially
Held |      | Percent of Preferred Stock Ownership
|---------------------------------------------------------------------- |  |  |  | --------------------------------------------------- | ------- | ------------------------------------- |  | -------------------------------------------------- | ---- | ------------------------------------
|Jong S.
Whang                                                          |  |  |  |                                                     | 278,472 | (4)                                   |  |                                                    | 9.6  | %                                   
|Robert T.
Hass                                                         |  |  |  |                                                     | 34,375  | (5)                                   |  |                                                    | 1.3  | %                                   
|Robert M.
Averick                                                      |  |  |  |                                                     | 10,000  | (6)                                   |  |                                                    | *    |                                     
|Lawrence D.
Firestone                                                  |  |  |  |                                                     |        |                                       |  |                                                    | *    |                                     
|Robert F.
King                                                         |  |  |  |                                                     | 5,667   | (7)                                   |  |                                                    | *    |                                     
|Directors and
Executive Officers of the Company as a group (5 persons) |  |  |  |                                                     | 328,514 | (8)                                   |  |                                                    | 11.1 | %                                   
|Robert
Sussman                                                         |  |  |  |                                                     | 202,500 | (9)                                   |  |                                                    | 7.5  | %                                   
|520 Madison
Avenue 41st Floor New York, NY 10022                       |  |  |  |                                                     |         |                                       |  |                                                    |      |                                     
|Richard L.
Scott                                                       |  |  |  |                                                     | 312,500 | (10)(6)                               |  |                                                    | 10.4 | %                                   
|700 11th Street, Suite 101 Naples, FL 34102                            |  |  |  |                                                     |         |                                       |  |                                                    |      |                                     
|Steven N.
Bronson                                                      |  |  |  |                                                     | 256,250 | (11)(12)                              |  |                                                    | 8.7  | %                                   
|100 Mill
Plain Road Danbury, CT 06811                                  |  |  |  |                                                     |         |                                       |  |                                                    |      |                                     






|* |  | Less than 1%.
|- |  | -------------

|(1) |  | Except as otherwise noted, 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 the Companys President, Chief Executive
Officer and a director. Mr. Hass is the Vice President  Finance, Chief Financial Officer, Treasurer, Secretary and a director. Messrs. Averick,
Firestone and King are directors of the Company. Messrs. Sussman, Scott and Bronson are beneficial owners of at least 5% of the Companys
outstanding Common Stock.
|--- |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|(3) |  | The share amounts and percentages shown include shares of Common
Stock actually owned as of January 20, 2006, 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, warrants or Preferred Stock. All shares of Common Stock that the identified person had the right to
acquire within 60 days of January 20, 2006, upon the exercise of options or warrants or the conversion of Preferred Stock, 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 (i) 351 shares held jointly with Mr. Whangs
spouse and (ii) 194,017 shares issuable upon exercise of options exercisable within 60 days of January 20, 2006.
|--- |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------

|(5) |  | Includes 34,250 shares issuable upon exercise of options
exercisable within 60 days of January 20, 2006.
|--- |  | --------------------------------------------------------------------------------------------------------



7


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|(6) |  | Mr. Averick may be deemed to beneficially own 10,000 shares of
Common Stock as a result of his 3.2% membership interest in Amtech Investments, LLC, which owns 312,500 shares of Preferred Stock that is convertible
into Common Stock. Richard L. Scott may be deemed to share beneficially ownership of such 10,000 shares of Common Stock as set forth in footnote 10
below.
|--- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|(7) |  | Includes 5,667 shares issuable upon exercise of options
exercisable within 60 days of January 20, 2006.
|--- |  | -------------------------------------------------------------------------------------------------------

|(8) |  | Includes 243,934 shares issuable upon exercise of options and
conversion of Preferred Stock exercisable or convertible, respectively, within 60 days of January 20, 2006.
|--- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|(9) |  | Includes 2,500 shares jointly owned with Mr. Sussmans
spouse.
|--- |  | --------------------------------------------------------------

|(10) |  | Mr. Scott is a controlling member of Amtech Investments, LLC, a
member-managed limited liability company which owns 312,500 shares of Preferred Stock that is convertible into Common Stock. Mr. Scott may be deemed to
share beneficial ownership of 10,000 shares of such Common Stock with Robert M. Averick as set forth in footnote 6 above.
|---- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|(11) |  | Mr. Bronson is president of Catalyst Financial LLC, a
broker-dealer that owns a warrant to purchase 60,000 shares of Common Stock.
|---- |  | ----------------------------------------------------------------------------------------------------------------------------------

|(12) |  | Mr. Bronson is managing member of Catalyst Fund GP, LLC, which
is the general partner of Catalyst Fund, L.P. Catalyst Fund, L.P. owns 196,250 shares of Preferred Stock.
|---- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|ITEM
13. |  | CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS
|-------- |  | ----------------------------------------------



Other than as set forth below,
the Company has had no transactions since the beginning of its last fiscal year with any director, director nominee, executive officer, security holder
known to the Company to own of record or beneficially more than 5% of the Common Stock, or any member of the immediate family of any of the foregoing
persons, in which the amount involved exceeded $60,000.




In April 2005, the Company
completed a private offering of 540,000 shares of Preferred Stock. Catalyst Financial, LLC (Catalyst Financial), which is the
Companys investment banker, served as the placement agent in connection with the private placement and received a cash fee of $172,800,
reimbursement of expenses of $43,200 and a warrant to purchase 60,000 shares of Common Stock as consideration for its services. In addition, Catalyst
Fund, L.P. acquired 196,250 shares of Preferred Stock in the private placement in consideration for $785,000. Steven N. Bronson, as president of
Catalyst Financial and the managing member of Catalyst Fund GP LLC, which is the general partner of Catalyst Fund, L.P., may be deemed to beneficially
own 256,250 shares of Common Stock, representing approximately 8.7% of the total shares of Common Stock issued and outstanding.


|ITEM
14. |  | PRINCIPAL ACCOUNTING FEES AND SERVICES
|-------- |  | --------------------------------------



The following table sets forth
the fees billed to us by our independent auditors during the years ended September 30, 2005 and 2004 for: (i) services rendered for the audit of our
annual financial statements and the review of our quarterly financial statements, (ii) services by our auditor that are reasonably related to the
performance of the audit or review of our financial statements and that are not reported as audit fees, (iii) services rendered in connection with tax
compliance, tax advice and tax planning, and (iv) all other fees for services rendered.







|                       |  |  |  | Year Ended Sept. 30, 2005 |         | Year Ended Sept. 30, 2004
|---------------------- |  |  |  | ------------------------- | ------- | -------------------------
|Audit
Fees             |  |  |  | $                         | 243,649 |                          
|Audit-Related
Fees (1) |  |  |  |                           | 6,000   |                          
|Tax
Fees               |  |  |  |                           |        |                          
|All Other
Fees         |  |  |  |                           |        |                          
|Total
Fees             |  |  |  | $                         | 249,649 |                          






|(1) |  | Accounting and reporting advisory services related to regulatory
filings and acquisition activities.
|--- |  | ----------------------------------------------------------------------------------------------------



8


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PRE-APPROVAL POLICY




In May 2003, the Audit Committee
adopted a Pre-Approval Policy (the Policy) governing the approval of all audit and non-audit services performed by the Companys
independent auditor in order to ensure that the performance of such services does not impair the auditors independence.




According to the Policy, the
Audit Committee will annually review and pre-approve the types of services, and will set a limit on the fees for such services, that may be provided by
the independent auditor during the following year. The Policy specifically describes the annual audit services and fees, other services that are
audit-related, the preparation of tax returns and tax related compliance services and all other services that have the general pre-approval of the
Audit Committee. The term of any general pre-approval is twelve (12) months from the date of pre-approval, unless the Audit Committee specifically
provides for a different period.




Any service to be provided by the
independent auditor that has not received general pre-approval under the Policy is required to be submitted to the Audit Committee for approval prior
to the commencement of a substantial portion of the engagement. Any proposed service exceeding pre-approved cost levels is also required to be
submitted to the Audit Committee for specific approval.




The Audit Committee will revise
the list of general pre-approved services from time to time based on subsequent determinations. The Audit Committee does not delegate its
responsibilities to pre-approve services performed by the independent auditor to management.




9


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PART IV


|ITEM
15. |  | EXHIBITS AND FINANCIAL STATEMENT SCHEDULES
|-------- |  | ------------------------------------------






|EXHIBIT NO. |  |  |  | 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.                 
|32.1        |  |  |  | Certification Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. Filed
herewith.
|32.2        |  |  |  | Certification Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. Filed
herewith.



10


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SIGNATURES




Pursuant to the requirements of
Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned,
thereunto duly authorized.




AMTECH SYSTEMS,
INC.




January 30, 2006


|By: |  | /s/ Jong S. Whang Jong
S. Whang, President and Chief Executive Officer
|--- |  | ----------------------------------------------------------------------



Pursuant to the
requirements of the Securities Exchange Act of 1934, this report on Form 10-K/A has been signed below by the following persons on behalf of the
registrant and in the capacities and on the dates indicated:







|SIGNATURE                                                |  |  |  | TITLE                                                                                                     |  | DATE            
|-------------------------------------------------------- |  |  |  | --------------------------------------------------------------------------------------------------------- |  | ----------------
|/s/ Jong S.
WhangJong S. Whang                           |  |  |  | Chairman of the Board, President and Chief Executive Officer (Principal Executive Officer)                |  | January 30,
2006
|/s/ Robert T.
HassRobert T. Hass                         |  |  |  | Vice
President  Finance, Chief Financial Officer and Director (Principal Financial & Accounting Officer) |  | January 30,
2006
|*Robert M. Averick                                       |  |  |  | Director                                                                                                  |  | January 30,
2006
|*Lawrence D. Firestone                                   |  |  |  | Director                                                                                                  |  | January 30,
2006
|*Robert F. King                                          |  |  |  | Director                                                                                                  |  | January 30,
2006
|*By:  /s/ Robert T. HassRobert T. Hass, attorney-in-fact |  |  |  |                                                                                                           |  |                 



11


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EXHIBIT INDEX







|EXHIBIT NO. |  |  |  | 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.                 
|32.1        |  |  |  | Certification Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. Filed
herewith.
|32.2        |  |  |  | Certification Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. Filed
herewith.



12


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