<PAGE>   1
                                                                     EXHIBIT 3.2



                          AMENDED AND RESTATED BY-LAWS
                                       OF
                               MICRION CORPORATION


                                    ARTICLE I

                                  STOCKHOLDERS


      SECTION 1. ANNUAL MEETING. The annual meeting of the stockholders shall be
held within six months after the end of the corporation's fiscal year on such
date, and at such place and time, as may be determined each year by the board of
directors. If in any year the annual meeting is not held within the period
specified above, a special meeting in lieu thereof may be held at a later time
and any elections held or business transacted at such meeting shall have the
same force and effect as if held or transacted at the annual meeting.

      SECTION 2. SPECIAL MEETINGS. Special meetings of the stockholders may be
called at any time by the president or by the board of directors and shall be
called by the clerk, or in case of the death, absence, incapacity or refusal of
the clerk, by any other officer, upon written application of one or more
stockholders who hold at least 40% in interest of the capital stock entitled to
vote thereat. Such application shall specify the purposes for which the meeting
is to be called and may designate the date, hour and place of such meeting,
provided, however, that no such application shall designate a date not a full
business day or an hour not within normal business hours as the date or hour of
such meeting without the approval of the president or the board of directors.

      SECTION 3. PLACE OF MEETINGS. Meetings of the stockholders may be held any
where within, but not without, the United States.

      SECTION 4. NOTICE. Except as hereinafter provided, a written or printed
notice of every meeting of stockholders stating the place, date, hour and
purposes thereof shall be given by the clerk or an assistant clerk (or by any
other officer in the case of an annual meeting or by the person or persons
calling the meeting in the case of a special meeting) at least seven (7) days
before the meeting to each stockholder entitled to vote thereat and to each
stockholder who, by law, by the articles of organization or by these by-laws, is
entitled to such notice, by leaving such notice with him or at his residence or
usual place of business or by mailing it, postage prepaid, addressed to him at
his address as it appears upon the records of the corporation. No notice of the
place, date, hour or purposes of any annual or special meeting of stockholders
need be given to a stockholder if a written waiver of such notice, executed
before or after the
<PAGE>   2
meeting by such stockholder or his attorney thereunto authorized, is filed with
the records of the meeting.

      SECTION 5. ACTION AT A MEETING. Except as otherwise provided by the
articles of organization, at any meeting of the stockholders a majority of all
shares of stock then issued, outstanding and entitled to vote (including shares
as to which a nominee has no voting authority as to certain matters brought
before the meeting) shall constitute a quorum for the transaction of business.
Though less than a quorum be present, any meeting may without further notice be
adjourned to a subsequent date or until a quorum be had, and at any such
adjourned meeting any business may be transacted which might have been
transacted which might have been transacted at the original meeting.

      When a quorum is present at any meeting, the affirmative vote of a
majority of the shares of stock present or represented and entitled to vote
shall be necessary and sufficient to the determination of such question, unless
a larger vote is required by law, by the articles of organization or by these
by-laws; provided, however, that any election by stockholders shall be
determined by a plurality of the votes cast by the stockholders entitled to vote
in such election. Shares as to which a nominee has no voting authority as to a
particular question or questions brought before the meeting will not be deemed
to be cast with respect to such question or questions.

      Except as otherwise provided by law or by the articles of organization or
by these by-laws, each holder of record of shares of stock entitled to vote on
any matter shall have one vote for each such share held of record by him and a
proportionate vote for any fractional shares so held by him. Stockholders may
vote either in person or by proxy. No proxy dated more than six months before
the meeting named therein shall be valid and no proxy shall be valid after the
final adjournment of such meeting. A proxy with respect to stock held in the
name of two or more persons shall be valid if executed by any one of them unless
at or prior to the exercise of the proxy the corporation receives a specific
written notice to the contrary from any one of them. A proxy purporting to be
executed by or on behalf of a stockholder shall be deemed valid unless
challenged at or prior to its exercise and the burden of proving its invalidity
shall rest on the challenger.

      Any election by stockholders and the determination of any other questions
to come before a meeting of the stockholders shall be by ballot if so requested
by any stockholder entitled to vote thereon but need not be otherwise.

      SECTION 6. ACTION WITHOUT A MEETING. Any action required or permitted to
be taken at any meeting of the stockholders may be taken without a meeting if
all stockholders entitled to vote


                                       2
<PAGE>   3
on the matter consent to the action in writing and the written consents are
filed with the records of the meetings of stockholders. Such consents shall be
treated for all purposes as a vote at a meeting.


                                   ARTICLE II

                                    DIRECTORS

      SECTION 1. NUMBER AND ELECTION. Except as otherwise provided by law or by
the articles of organization, the number of directors for the ensuing year shall
be determined from time to time by the board of directors and shall be elected
at the annual meeting of the stockholders by such stockholders as have the right
to vote thereon. No decrease in the number of directors constituting the board
of directors shall shorten the term of any incumbent director.

      SECTION 2. TERM. The provisions of Chapter 156B, Section 50A of the
Massachusetts General Laws with respect to staggered terms for directors shall
apply to this corporation. Commencing with the first annual meeting of the
stockholders following June 30, 1997 (the "Commencement Meeting"), the directors
of this corporation shall be classified, with respect to the time for which they
severally hold office, into three classes, as nearly equal in number as
possible; the term of office of those of the first class ("Class I Directors")
to continue until the first annual meeting of stockholders following the
Commencement Meeting and until their successors are duly elected and qualified;
the term of office of those of the second class ("Class II Directors") to
continue until the second annual meeting of stockholders following the
Commencement Meeting and until their successors are duly elected and qualified;
and the term of office of those of the third class ("Class III Directors") to
continue until the third annual meeting of stockholders following the
Commencement Meeting and until their successors are duly elected and qualified.
At each annual meeting of stockholders, the successors to the class of directors
whose term expires at that meeting shall be elected to hold office for a term
continuing until the annual meeting held in the third year following the year of
their election and until their successors are duly elected and qualified.

      SECTION 3. RESIGNATIONS. Any director may resign by delivering his or her
written resignation to the corporation at its principal office or to the
president or clerk or, if there be one, to the secretary. Such resignation shall
become effective at the time or upon the happening of the condition, if any,
specified therein or, if no such time or condition is specified, upon its
receipt.


                                       3
<PAGE>   4
      SECTION 4. REMOVAL. At any meeting of the stockholders called for the
purpose, any director may be removed from office only for cause (as defined in
Section 50A of Chapter 156B of the Massachusetts General Laws) by the
affirmative vote of a majority of the shares issued, outstanding and entitled to
vote in the election of directors. At any meeting of the board of directors, any
director may be removed from office for cause by vote of a majority of the
directors then in office.

      SECTION 5. VACANCIES. Vacancies and newly created directorships, whether
resulting from an increase in the size of the board of directors, from the
death, resignation, disqualification or removal of a director or otherwise,
shall be filled solely by the affirmative vote of a majority of directors then
in office, even though less than a quorum of the board of directors. Any
director elected in accordance with this Section 5 shall hold office for the
remainder of the full term of the class of directors in which the vacancy
occurred or the new directorship was created and until such director's successor
shall have been elected and qualified.

      SECTION 6. REGULAR MEETINGS. Regular meetings of the board of directors
may be held at such times and places within or without The Commonwealth of
Massachusetts as the board of directors may fix from time to time and, when so
fixed, no notice thereof need be given. The first meeting of the board of
directors following the annual meeting of the stockholders shall be held without
notice immediately after and at the same place as the annual meeting of the
stockholders or the special meeting held in lieu thereof. If in any year a
meeting of the board of directors is not held at such time and place, any
elections to be held or business to be transacted at such meeting may be held or
transacted at any later meeting of the board of directors with the same force
and effect as if held or transacted at such meeting.

      SECTION 7. SPECIAL MEETINGS. Special meetings of the board of directors
may be called at any time by the president or secretary (or, if there be no
secretary, the clerk) or by any director. Such special meetings may be held
anywhere within or without The Commonwealth of Massachusetts. A written, printed
or telegraphic notice stating the place, date and hour (but not necessarily the
purposes) of the meeting shall be given by the secretary or an assistant
secretary (or, if there be no secretary or assistant secretary, the clerk or an
assistant clerk) or by the officer or director calling the meeting at least
forty-eight (48) hours before such meeting to each director by leaving such
notice with him or at his residence or usual place of business or by mailing it,
postage prepaid, or sending it by prepaid telegram, addressed to him at his last
known address. No notice of the place, date or hour of any meeting of the board
of directors need be given to any director if a written waiver of





                                       4
<PAGE>   5
such notice, executed by him before or after the meeting, is filed with the
records of the meeting, or to any director who attends the meeting without
protesting prior thereto or at its commencement the lack of notice to him.

      SECTION 8. ACTION AT A MEETING. At any meeting of the board of directors,
a majority of the directors then in office shall constitute a quorum. Though
less than a quorum be present, any meeting may without further notice be
adjourned to a subsequent date or until a quorum be had. When a quorum is
present at any meeting a majority of the directors present may take any action
on behalf of the board except to the extent that a larger number is required by
law, by the articles of organization or by these by-laws.

      SECTION 9. ACTION WITHOUT A MEETING. Any action required or permitted to
be taken at any meeting of the directors may be taken without a meeting if all
the directors consent to the action in writing and the written consents are
filed with the records of the meetings of the directors. Such consents shall be
treated for all purposes as a vote at a meeting.

      SECTION 10. POWERS. The board of directors shall have and may exercise all
the powers of the corporation, except such as by law, by the articles of
organization or by these by-laws are conferred upon or reserved to the
stockholders. In the event of any vacancy in the board of directors, the
remaining directors then in office, except as otherwise provided by law, shall
have and may exercise all of the powers of the board of directors until the
vacancy is filled.

      SECTION 11. COMMITTEES. The board of directors may elect from the board an
executive committee or one or more other committees and may delegate to any such
committee or committees any or all of the powers of the board except those which
by law, by the articles of organization or by these by-laws may not be so
delegated. Such committees shall serve at the pleasure of the board of
directors. Except as the board of directors may otherwise determine, each such
committee may make rules for the conduct of its business, but, unless otherwise
determined by the board or in such rules, its business shall be conducted as
nearly as may be as is provided in these by-laws for the conduct of the business
of the board of directors.

      SECTION 12. MEETING BY TELECOMMUNICATIONS. Members of the board of
directors or any committee elected thereby may participate in a meeting of such
board or committee by means of a conference telephone or similar communications
equipment by means of which all persons participating in a meeting can hear each
other at the same time and participation by such means shall constitute presence
in person at the meeting.




                                       5
<PAGE>   6
                                   ARTICLE III

                                    OFFICERS

      SECTION 1. ENUMERATION. The officers of the corporation shall consist of a
president, a treasurer and a clerk and such other officers, including without
limitation a chairman of the board of directors, a secretary and one or more
vice presidents, assistant treasurers, assistant clerks and assistant
secretaries, as the board of directors may from time to time determine.

      SECTION 2. QUALIFICATIONS. No officer need be a stockholder or a director.
The same person may hold at the same time one or more offices unless otherwise
provided by law. The clerk shall be a resident of Massachusetts unless the
corporation shall have a resident agent. Any officer may be required by the
board of directors to give a bond for the faithful performance of his duties in
such form and with such sureties as the board may determine.

      SECTION 3. ELECTIONS. The president, treasurer and clerk shall be elected
annually by the board of directors at its first meeting following the annual
meeting of the stockholders. All other officers shall be chosen or appointed by
the board of directors.

      SECTION 4. TERM. Except as otherwise provided by law, by the articles of
organization or by these by-laws, the president, treasurer and clerk shall hold
office until the first meeting of the board of directors following the next
annual meeting of the stockholders and until their respective successors are
chosen and qualified. All other officers shall hold office until the first
meeting of the board of directors following the next annual meeting of the
stockholders, unless a shorter time is specified in the vote choosing or
appointing such officer or officers.

      SECTION 5. RESIGNATIONS. Any officer may resign by delivering his written
resignation to the corporation at its principal office or to the president or
clerk, or, if there be one, to the secretary. Such resignation shall be
effective at the time or upon the happening of the condition, if any, specified
therein or, if no such time or condition is specified, upon its receipt.

      SECTION 6. REMOVAL. Any officer may be removed from office with or without
cause by vote of a majority of the directors then in office. An officer may be
removed for cause only after a reasonable notice and opportunity to be heard
before the board of directors.

      SECTION 7. VACANCIES. Vacancies in any office may be filled by the board
of directors.


                                       6
<PAGE>   7
      SECTION 8. CERTAIN DUTIES AND POWERS. The officers designated below,
subject at all times to these by-laws and to the direction and control of the
board of directors, shall have and may exercise the respective duties and powers
set forth below:

            THE CHAIRMAN OF THE BOARD OF DIRECTORS. The chairman of the board of
      directors, if there be one, shall, when present, preside at all meetings
      of the board of directors.

            THE PRESIDENT. The president shall be the chief executive officer of
      the corporation and shall have general operating charge of its business.
      Unless otherwise prescribed by the board of directors, he shall, when
      present, preside at all meetings of the stockholders, and, if a director,
      at all meetings of the board of directors unless there be a chairman of
      the board of directors who is present at the meeting.

            THE TREASURER.  The treasurer shall be the chief financial officer 
      of the corporation and shall cause to be kept accurate books of account.

            THE CLERK. The clerk shall keep a record of all proceedings of the
      stockholders and, if there be no secretary, shall also keep a record of
      all proceedings of the board of directors. In the absence of the clerk
      from any meeting of the stockholders or, if there be no secretary, from
      any meeting of the board of directors, an assistant clerk, if there be
      one, otherwise a clerk pro tempore designated by the person presiding at
      the meeting, shall perform the duties of the clerk at such meeting.

            THE SECRETARY. The secretary, if there be one, shall keep a record
      of all proceedings of the board of directors. In the absence of the
      secretary, if there be one, from any meeting of the board of directors, an
      assistant secretary, if there be one, otherwise a secretary pro tempore
      designated by the person presiding at the meeting, shall perform the
      duties of the secretary at such meeting.

      SECTION 9. OTHER DUTIES AND POWERS. Each officer, subject at all times to
these by-laws and to the direction and control of the board of directors, shall
have and may exercise, in addition to the duties and powers specifically set
forth in these by-laws, such duties and powers as are prescribed by law, such
duties and powers as are commonly incident to his office and such duties and
powers as the board of directors may from time to time prescribe.






                                       7
<PAGE>   8
                                   ARTICLE IV

                                  CAPITAL STOCK

      SECTION 1. AMOUNT AND ISSUANCE. The total number of shares and the par
value, if any, of each class of stock which the corporation is authorized to
issue shall be stated in the articles of organization. The directors may at any
time issue all or from time to time any part of the unissued capital stock of
the corporation from time to time authorized under the articles of organization,
and may determine, subject to any requirements of law, the consideration for
which stock is to be issued and the manner of allocating such consideration
between capital and surplus.

      SECTION 2. CERTIFICATES. Each stockholder shall be entitled to a
certificate or certificates stating the number and the class and the designation
of the series, if any, of the shares held by him, and otherwise in form approved
by the board of directors. Such certificate or certificates shall be signed by
the president or a vice president and by the treasurer or an assistant
treasurer. Such signatures may be facsimiles if the certificate is signed by a
transfer agent, or by a registrar, other than a director, officer or employee of
the corporation. In case any officer who has signed or whose facsimile signature
has been placed on such certificate shall have ceased to be such officer before
such certificate is issued, it may be issued by the corporation with the same
effect as if he were such officer at the time of its issue.

      Every certificate issued for shares of stock at a time when such shares
are subject to any restriction on transfer pursuant to the articles of
organization, these by-laws or any agreement to which the corporation is a party
shall have the restriction noted conspicuously on the certificate and shall also
set forth on the face or back of the certificate either (i) the full text of the
restriction or (ii) a statement of the existence of such restriction and a
statement that the corporation will furnish a copy thereof to the holder of such
certificate upon written request and without charge.

      Every certificate issued for shares of stock at a time when the
corporation is authorized to issue more than one class or series of stock shall
set forth on the face or back of the certificate either (i) the full text of the
preferences, voting powers, qualifications and special and relative rights of
the shares of each class and series, if any, authorized to be issued, as set
forth in the articles of organization or (ii) a statement of the existence of
such preferences, powers, qualifications and rights and a statement that the
corporation will furnish a copy thereof to the holder of such certificate upon
written request and without charge.



                                       8
<PAGE>   9
      SECTION 3. TRANSFERS. The board of directors may make such rules and
regulations not inconsistent with the law, with the articles of organization or
with these by-laws as it deems expedient relative to the issue, transfer and
registration of stock certificates. The board of directors may appoint a
transfer agent and a registrar of transfers or either and require all stock
certificates to bear their signatures. Except as otherwise provided by law, by
the articles of organization or by these by-laws, the corporation shall be
entitled to treat the record holder of any shares of stock as shown on the books
of the corporation as the holder of such shares for all purposes, including the
right to receive notice of and to vote at any meeting of stockholders and the
right to receive any dividend or other distribution in respect of such shares.

      SECTION 4. RECORD DATE. The board of directors may fix in advance a time,
which shall be not more than sixty (60) days before the date of any meeting of
stockholders or the date for the payment of any dividend or the making of any
distribution to stockholders or the last day on which the consent or dissent of
stockholders may be effectively expressed for any purpose, as the record date
for determining the stockholders having the right to notice of and to vote at
such meeting and any adjournment thereof or the right to receive such dividend
or distribution or the right to give such consent or dissent, and in such case
only stockholders of record on such record date shall have such right,
notwithstanding any transfer of stock on the books of the corporation after the
record date; or without fixing such record date the directors may for any of
such purposes close the transfer books for all or any part of such period.

      SECTION 5. LOST CERTIFICATES. The board of directors may, except as
otherwise provided by law, determine the conditions upon which a new certificate
of stock may be issued in place of any certificate alleged to have been lost,
mutilated or destroyed.


                                    ARTICLE V

                            MISCELLANEOUS PROVISIONS

      SECTION 1. FISCAL YEAR. The fiscal year of the corporation shall begin on
the first day of July in each year and end on the last day of June next
following.

      SECTION 2. CORPORATE SEAL. The seal of the corporation shall be in such
form as shall be determined from time to time by the board of directors.

      SECTION 3. CORPORATION RECORDS. The original, or attested copies, of the
articles of organization, by-laws and records of


                                       9
<PAGE>   10
all meetings of the incorporators and stockholders, and the stock and transfer
records, which shall contain the names of all stockholders and the record
address and the amount of stock held by each, shall be kept in The Commonwealth
of Massachusetts at the principal office of the corporation in said Commonwealth
or at an office of the transfer agent or of its clerk or of its resident agent,
if any. Said copies and records need not all be kept in the same office. They
shall be available at all reasonable times to inspection by any stockholder for
any proper purpose but not if the purpose for which such inspection is sought is
to secure a list of stockholders or other information for the purpose of selling
said list or information or copies thereof or of using the same for a purpose
other than the interest of the applicant, as a stockholder, relative to the
affairs of the corporation.

      SECTION 4. VOTING OF SECURITIES. Except as the board of directors may
otherwise prescribe, the president or the treasurer shall have full power and
authority in the name and on behalf of the corporation, subject to the
instructions of the board of directors, to waive notice of, to attend, act and
vote at, and to appoint any person or persons to act as proxy or attorney in
fact for this corporation (with or without power of substitution) at any meeting
of stockholders or shareholders of any other corporation or organization, the
securities of which may be held by this corporation.


                                   ARTICLE VI

                                   AMENDMENTS

      These by-laws may be amended or repealed at any annual or special meeting
of the stockholders by the affirmative vote of a majority of the shares of
capital stock then issued, outstanding and entitled to vote provided notice of
the proposed amendment or repeal is given in the notice of the meeting.

      If authorized by the articles or organization, these by-laws may also be
amended or repealed in whole or in part, or new by-laws made, by the board of
directors except with respect to any provision hereof which by law, the articles
of organization or these by-laws requires action by the stockholders. Not later
than the time of giving notice of the meeting of stockholders next following the
making, amendment or repeal by the directors of any by-laws, notice thereof
stating the substance of such change shall be given to all stockholders entitled
to vote on amending the by-laws. Any by-law to be made, amended or repealed by
the directors may be amended or repealed by the stockholders.


                                       10