**Exhibit 31.2**

AMTECH SYSTEMS, INC. AND ITS
SUBSIDIARIESCERTIFICATION PURSUANT TO RULE 13a-14(a)/15d-14(a)OF THE
SECURITIES EXCHANGE ACT OF 1934, AS AMENDED

I, Bradley C. Anderson, certify
that:

1.I have reviewed this Annual Report
on Form 10-K of Amtech Systems, Inc. (the registrant),

2.Based on my knowledge, this report
does not contain any untrue statement of a material fact or omit to state a
material fact necessary to make the statements made, in light of the
circumstances under which such statements were made, not misleading with respect
to the period covered by this report;

3.Based on my knowledge, the financial
statements, and other financial information included in this report, fairly
present in all material respects the financial position, results of operations
and cash flows of the registrant as of, and for, the periods presented in this
report;

4.The registrants other certifying
officer and I are responsible for establishing and maintaining disclosure
controls and procedures (as defined in Exchange Act Rules 13a-15(e) and
15d-15(e)) for the registrant and we have:

(a)Designed such disclosure controls
and procedures, or caused such disclosure controls and procedures to be designed
under our supervision, to ensure that material information relating to the
registrant, including its consolidated subsidiaries, is made known to us by
others within those entities, particularly during the period in which this
report is being prepared;

(b) Evaluated the effectiveness of the
registrants disclosure controls and procedures and presented in this report our
conclusions about the effectiveness of the disclosure controls and procedures,
as of the end of the period covered by this report based on such evaluation;
and

(c)Disclosed in this report any change
in the registrants internal control over financial reporting that occurred
during the registrants most recent fiscal quarter (the registrants fourth
fiscal quarter in the case of an annual report) that has materially affected, or
is reasonably likely to materially affect, the registrants internal control
over financial reporting; and

5.The registrants other certifying
officer and I have disclosed, based on our most recent evaluation of internal
control over financial reporting, to the registrants auditors and the audit
committee of registrants board of directors (or persons performing the
equivalent functions):

(a)All significant deficiencies and
material weaknesses in the design or operation of internal control over
financial reporting which are reasonably likely to adversely affect the
registrants ability to record, process, summarize and report financial
information; and

(b)Any fraud, whether or not material,
that involves management or other employees who have a significant role in the
registrants internal control over financial reporting.

|By |  | /s/ Bradley C.
Anderson                                    |  | 
|-- |  | ---------------------------------------------------------- |  | 
|   |  | Bradley C. Anderson                                       
|   |  | Vice President 
      Finance and Chief Financial Officer | 
|   |  | Amtech
      Systems, Inc.                                
|   |  | Date:
      December 12, 2007