<PAGE>

                                                                    EXHIBIT 10.6
                                                                    ------------
May 30, 2001

Paul Doscher
209 Fieldcrest Court
Danville, CA.  94506


                        SEPARATION AGREEMENT AND RELEASE
                        --------------------------------

Dear Paul:

This letter agreement ("Agreement") sets forth the arrangements we have made
with respect to your separation from Entrust Technologies Inc. The arrangements
will be as follows:

1.  As used in this Agreement, the term "ENTRUST" and/or "Company" shall mean
    Entrust Technologies Inc., its parent, subsidiaries (including enCommerce,
    Inc.), affiliates, successors, assigns; all past and present officers,
    directors, employees and agents (in their individual and representative
    capacities) of ENTRUST.

2.  Provided that you comply with all material aspects of this Agreement, your
    employment relationship with ENTRUST shall continue until the close of
    business on August 4, 2001. Thereafter, your employment relationship with
    ENTRUST will be ended and will not resume. However, after June 4, 2001, your
    duties as an employee shall cease, with the exception of assisting in the
    transition of your responsibilities to other ENTRUST employees and, upon
    request, providing strategic advice to ENTRUST's executive team for a period
    of sixty (60) days. The sixty (60) day period provided for in paragraph two
    (2) shall constitute your WARN notice period pursuant to the WARN notice
    attached hereto as schedule A.

3.  You acknowledge and represent that a time period of twenty-one (21) calendar
    days has been provided to you in order for you to consider the subject
    matter of this Agreement and that the Company has advised you to consult
    with an attorney of your choice prior to signing this Agreement. In
    addition, you acknowledge that you will have seven (7) calendar days
    following the execution of this document to revoke this Agreement by written
    notice. To be valid, the letter of revocation must be received by Mr. Jeff
    Bearrows, Vice President, Human Resources, Entrust Technologies, Inc., 4975
    Preston Park Blvd., Suite 400, Plano, TX 75093, not later than the close of
    business seven (7) calendar days after you sign this Agreement. This
    Agreement is effective after it has been signed by both parties and after
    eight (8) days have passed since Employee has signed the Agreement, unless
    revoked by Employee within seven (7) days after the date the Agreement was
    signed by Employee.

4.  Following your return to the Company of an executed agreement and the
    expiration of the seven (7) day revocation period, or on August 4, 2001,
    whichever is later, the Company shall make a severance payment to you
    calculated as follows:
<PAGE>

i.)   $150,000.00, reflecting 6 months of base pay and bonus;

ii.)  $4,236.18 reflecting the amount equal to the cost of you maintaining your
      current group health and dental coverage pursuant to the Consolidated
      Omnibus Budget Reconciliation Act of 1985 ("COBRA") for six months;

iii.) $12,233.69, reflecting 128.26 hours of earned but untaken vacation;

iv.)  You will be allowed to retain your laptop computer.


5.  With respect to any monies or monetary equivalents to be paid hereunder,
    Entrust shall be free to withhold whatever amounts it shall reasonably
    determine to be appropriate concerning any and all applicable federal, state
    and local tax withholding.

6.  With respect to your stock option grants, 50% of the unvested stock option
    grants under either of the ENTRUST Amended and Restated 1996 Stock Incentive
    Plan shall vest on August 4, 2001. In addition, 100% of the unvested stock
    option grants under the enCommerce, Inc. 1997 Stock Option Plan shall vest
    on August 4, 2001.You will have the right to exercise any vested options for
    up to 3 months after August 4, 2001. During the period of June 4, 2001
    through August 4, 2001, you will continue normally vesting in currently held
    options.

7.  All ENTRUST company provided benefits not expressly extended to you pursuant
    to this Agreement shall be terminated effective 12:01 a.m. September 1,
    2001. However, continued health cverage will be offered as required by the
    Consolidated Omnibus Budget Reconciliation Act of 1985 ("COBRA"), for the
    period required by law following the date of your separation from the
    ENTRUST.

8.  After June 4, 2001, you shall seek prior approval before incurring any
    expenses or making a commitment on behalf of Entrust. You shall reconcile
    and settle, as soon as possible, and in no event later than June 15, 2001,
    any expenses incurred by you in connection with ENTRUST business for which
    you are entitled to reimbursement.

9.  You agree that you will not act in any manner that might damage the business
    of the Company. You agree that you will not counsel or assist any attorneys
    or their clients in the presentation or prosecution of any disputes,
    differences, grievances, claims, charges, or complaints by any third party
    against the Company and/or any officer, director, employee, agent,
    representative, shareholder or attorney of the Company, unless under a
    subpoena or other court order to do so. Specifically, you agree not to
    comment on the matter of the class action lawsuit referred to as In re
    Entrust Securities Litigation, No. 2-00-CV-119-TJW (E.D. Tex.). Without
    ENTRUST's prior consent you also agree not to discuss the litigation with
    the plaintiffs, their attorneys, or their representatives, or to cooperate
    with the plaintiffs. You further agree both to immediately notify the
    Company upon receipt of any court order, subpoena, or any legal discovery
    device that seeks or might require the disclosure or production of the
    existence or terms of this Agreement, and to furnish, within three (3)
    business days of its receipt, a copy of such subpoena or legal discovery
    device to the Company. The Parties also agree to refrain from any
<PAGE>

     defamation, libel or slander of the other Party or tortious interference
     with the contracts and relationships of the other Party.

10.  You agree that for a period of twelve (12) months immediately following the
     termination of your relationship with ENTRUST for any reason, whether with
     or without good cause or for any or no cause, at the option either of
     ENTRUST or yourself, with or without notice, you shall not either directly
     or indirectly solicit, induce, recruit or encourage any of ENTRUST'S
     employees to leave their employment, or take away such employees, or
     attempt to solicit, induce, recruit, encourage or take away employees of
     ENTRUST, either for yourself or for any other person or entity.

11.  You hereby recognize and reaffirm the promises and obligations in the Non-
     Competition Agreement and Intellectual Property and Confidentiality
     Agreement executed by you on or about April 18, 2000.

12.  You agree that for twelve (12) months following the Effective Date, you
     will not, without the prior written consent of the Company, (i) serve as a
     partner, employee, consultant, officer, director, manager, agent,
     associate, investor, or (ii) directly or indirectly, own, purchase,
     organize or take preparatory steps for the organization of, or (iii) build,
     design, finance, acquire, lease, operate, manage, invest in, work or
     consult for or otherwise affiliate yourself with any of the following
     businesses: Netegrity, RSA, and VeriSign. The foregoing covenant shall
     cover your activities in every part of the Territory in which you conducted
     business on behalf of the Company during your employment with the Company.
     "Territory" shall mean (i) all counties in the State of California, (ii)
     all other states of the United States of America and (iii) all other
     countries of the world; provided that, with respect to clauses (ii) and
     (iii), the Company derives at least five percent (5%) of its gross revenues
     from such geographic area prior to the date of the termination of my
     relationship with the Company. You acknowledge that your fulfillment of the
     obligations contained in this provision is necessary to protect the
     Company's confidential information and, consequently, to preserve the value
     and goodwill of the Company. You further acknowledge the time, geographic
     and scope limitations of this obligation are reasonable, especially in
     light of the Company's desire to protect its confidential information, and
     that you will not be precluded from gainful employment you are obligated
     not to compete with the Company during the period, with the companies, and
     within the Territory as described above. The covenant described above shall
     be construed as a series of separate covenants, one for each city, county
     and state of any geographic area in the Territory. Except for geographic
     coverage, each such separate covenant shall be deemed identical in terms to
     the covenant contained above. If, in any judicial proceeding, a court
     refuses to enforce any of such separate covenants (or any part thereof),
     then such unenforceable covenant (or such part) shall be eliminated from
     this agreement to the extent necessary to permit the remaining separate
     covenants (or portions thereof) to be enforced. In the event the provisions
     above are deemed to exceed the time, geographic or scope limitations
     permitted by California law, then such provisions shall be reformed to the
     maximum time, geographic or scope limitations, as the case may be, then
     permitted by such law.
<PAGE>

13.  You agree that this Agreement is a confidential document as are all the
     terms and conditions expressed herein. Accordingly, you agree that you will
     not directly or indirectly disclose, publicize or discuss this Agreement,
     including its terms and/or conditions, with any employee and/or former
     employee of ENTRUST or any other person except your immediate family
     members, attorney, accountant, financial advisor, and/or outplacement
     advisor. In the event that you discuss this Agreement with any of the
     aforementioned individuals, it shall be your duty, responsibility and
     obligation to advise said individual(s) of the confidential nature of this
     Agreement and direct them not to discuss the terms and/or conditions of
     this Agreement with any other person. Notwithstanding the foregoing, this
     obligation of confidentiality shall cease in respect of those parts of the
     Agreement that are publicly disclosed by ENTRUST.

14.  You shall return to ENTRUST any and all property of ENTRUST and/or
     affiliates currently in your possession and/or subject to your control
     including, but not limited to, any and all computer equipment, facsimile
     machine, credit cards, identification cards, files, memoranda,
     correspondence, compensation surveys, drawings, designs, financial records,
     customer lists, personnel files, personnel lists or the like, whether such
     materials shall be written instruments or tapes in electronic and/or
     recorded format.

15.  Upon reasonable request, you shall make available to ENTRUST advice,
     assistance and information related to your former job duties, including,
     but not be limited to, offering and explaining evidence and providing sworn
     statements(s), deposition testimony and trial testimony as may be deemed
     necessary by ENTRUST for the preparation of its position in any legal
     proceedings(s) involving issues brought against or initiated by ENTRUST of
     which you have knowledge. In the event it is necessary for you to provide
     the aforementioned services, then ENTRUST shall reimburse you for
     authorized reasonable and documented travel expenses including, but not
     limited to, transportation, lodging and meals.

16.  You agree that the foregoing consideration represents settlement in full of
     all outstanding obligations owed to you by the Company. You, on your own
     behalf, and on behalf of your respective heirs, family members, executors,
     and assigns, hereby fully and forever releases the Company and its
     officers, directors, employees, investors, shareholders, administrators,
     affiliates, divisions, subsidiaries, predecessor and successor
     corporations, and assigns, from, and agree not to sue concerning, any
     claim, duty, obligation or cause of action relating to any matters of any
     kind, whether presently known or unknown, suspected or unsuspected, that
     you may possess arising from any omissions, acts or facts that have
     occurred up until and including the Effective Date of this Agreement
     including, without limitation: any and all claims relating to or arising
     from your employment relationship with the Company and the termination of
     that relationship; any and all claims relating to, or arising from, your
     right to purchase, or actual purchase of shares of stock of the Company,
     including, without limitation, any claims for fraud, misrepresentation,
     breach of fiduciary duty, breach of duty under applicable state corporate
     law, and securities fraud under any state or federal law; any and all
     claims under the law of any jurisdiction including, but not limited to,
     wrongful discharge of employment; constructive discharge from employment;
     termination in violation of public policy; discrimination;
<PAGE>

     breach of contract, both express and implied; breach of a covenant of good
     faith and fair dealing, both express and implied; promissory estoppel;
     negligent or intentional infliction of emotional distress; negligent or
     intentional misrepresentation; negligent or intentional interference with
     contract or prospective economic advantage; unfair business practices;
     defamation; libel; slander; negligence; personal injury; assault; battery;
     invasion of privacy; false imprisonment; and conversion; any and all claims
     for violation of any federal, state or municipal statute, including, but
     not limited to, Title VII of the Civil Rights Act of 1964, the Civil Rights
     Act of 1991, the Age Discrimination in Employment Act of 1967, the
     Americans with Disabilities Act of 1990, the Fair Labor Standards Act, the
     Employee Retirement Income Security Act of 1974, The Worker Adjustment and
     Retraining Notification Act, Older Workers Benefit Protection Act; the
     California Fair Employment and Housing Act, and Labor Code section 201, et
     seq. and section 970, et seq.; any and all claims for violation of the
     federal, or any state, constitution; any and all claims arising out of any
     other laws and regulations relating to employment or employment
     discrimination; any claim for any loss, cost, damage, or expense arising
     out of any dispute over the non-withholding or other tax treatment of any
     of the proceeds received by you as a result of this Agreement; and any and
     all claims for attorneys' fees and costs.

        The Company and you agree that the release set forth in this section
     shall be and remain in effect in all respects as a complete general release
     as to the matters released. This release does not extend to any obligations
     incurred under this Agreement. You acknowledge and agree that any breach of
     any provision of this Agreement shall constitute a material breach of this
     Agreement and shall entitle the Company immediately to recover the
     severance benefits provided to you under this Agreement. You shall also be
     responsible to the Company for all costs, attorneys' fees and any and all
     damages incurred by the Company (a) enforcing the obligation, including the
     bringing of any suit to recover the monetary consideration, and (b)
     defending against a claim or suit brought or pursued by you in violation of
     this provision.


17.  YOU ACKNOWLEDGE THAT YOU HAVE READ AND UNDERSTAND SECTION 1542 OF THE
     CALIFORNIA CIVIL CODE WHICH READS AS FOLLOWS: "A GENERAL RELEASE DOES NOT
     EXTEND TO CLAIMS WHICH THE CREDITOR DOES NOT KNOW OR SUSPECT TO EXIST IN
     HIS FAVOR AT THE TIME OF EXECUTING THE RELEASE, WHICH IF KNOWN BY HIM MUST
     HAVE MATERIALLY AFFECTED HIS SETTLEMENT WITH THE DEBTOR." YOU HEREBY
     EXPRESSLY WAIVE AND RELINQUISH ALL RIGHTS AND BENEFITS UNDER THAT SECTION
     AND ANY LAW OF ANY JURISDICTION OF SIMILAR EFFECT WITH RESPECT TO MY
     RELEASE OF ANY CLAIMS YOU MAY HAVE AGAINST THE COMPANY.

18.  YOU ACKNOWLEDGE THAT YOU HAVE READ THIS SEPARATION AGREEMENT / RELEASE AND
     THAT YOU UNDERSTAND ALL OF ITS TERMS AND EXECUTE IT VOLUNTARILY WITH FULL
     KNOWLEDGE OF ITS SIGNIFICANCE AND THE CONSEQUENCES THEREOF. FURTHER, YOU
     ACKNOWLEDGE THAT YOU HAVE HAD AN ADEQUATE OPPORTUNITY TO
<PAGE>

     REVIEW AND CONSIDER THE TERMS OF THIS SEPARATION AGREEMENT AND RELEASE,
     INCLUDING, AT YOUR DISCRETION, THE RIGHT TO DISCUSS THIS DOCUMENT WITH
     LEGAL COUNSEL OF YOUR CHOICE. FINALLY, YOU HEREBY ACKNOWLEDGE THAT YOU
     INTEND TO GRANT TO COMPANY A FULL AND FINAL RELEASE AS SET FORTH HEREIN.

19.  The Parties understand and acknowledge that this Agreement constitutes a
     compromise and settlement of disputed claims. No action taken by the
     Parties hereto, or either of them, either previously or in connection with
     this Agreement shall be deemed or construed to be: an admission of the
     truth or falsity of any claims heretofore made or an acknowledgment or
     admission by either party of any fault or liability whatsoever to the other
     party or to any third party.

20.  Except as expressly provided to the contrary or as precluded by operation
     of law, this Agreement shall be binding upon, and inure to the benefit of,
     you and your heirs, administrators, representative, executors, successors,
     and assigns and its enforceability shall not be challenged by such
     individuals.

21.  The terms and conditions of this Agreement will be open for your review and
     consideration through the close of business on June 8, 2001. If you have
     not returned an executed copy of this Agreement by facsimile or an original
     to Mr. Jeff Bearrows, at the address referenced in paragraph 5 of this
     Agreement, by the close of business by or on June 8, 2001, then the terms
     and conditions set forth in this Agreement shall be withdrawn as of that
     time and date.

22.  This Agreement constitutes the entire understanding of the parties with
     respect to the subject matter hereof and there are no promises,
     understandings or representations other than those set forth herein. This
     Agreement may be modified only with a written instrument duly executed by
     each of the parties. This agreement supercedes all other agreements or
     understanding with respect to your employment with respect to the subject
     matter hereof.

23.  The Parties agree that any and all disputes arising out of the terms of
     this Agreement, their interpretation, and any of the matters herein
     released, shall be subject to binding arbitration in Santa Clara County
     before the American Arbitration Association under its Employment Dispute
     Resolution Rules, or by a judge to be mutually agreed upon. The Parties
     agree that the prevailing party in any arbitration shall be entitled to
     injunctive relief in any court of competent jurisdiction to enforce the
     arbitration award. The Parties agree that the prevailing party in any
     arbitration shall be awarded its reasonable attorneys' fees and costs. The
     Parties hereby agree to waive their right to have any dispute between them
     resolved in a court of law by a judge or jury. This section 23 will not
     prevent either party from seeking injunctive relief (or any other
     provisional remedy) from any court having jurisdiction over the parties and
     the subject matter of their dispute relating to Employee's obligations
     under this Agreement and the agreements incorporated herein by reference.
<PAGE>

24.  This Agreement shall be deemed to have been executed and delivered within
     the State of California, and it shall be construed, interpreted, governed,
     and enforced in accordance with the laws of the State of California,
     without regard to choice of law principles. Any action at law, suit in
     equity, or other judicial proceedings for the enforcement of this
     Agreement, or related to any provision of this Agreement, shall be
     instituted only in courts with venue in the State of California, except
     that the Company may seek injunctive relief in any court having
     jurisdiction for any claim relating to the alleged misuse or
     misappropriation of the Company's trade secrets or confidential or
     proprietary information. Employee hereby expressly consents to venue and
     personal jurisdiction of the state and federal courts in the State of
     California for any lawsuit filed there against Employee by the Company
     arising from or relating to this Agreement.

25.  This Agreement shall in all respects be interpreted, enforced and governed
     under the laws of the State of California.

26.  If any provision of this Agreement shall be determined to be invalid,
     illegal, or unenforceable, in whole or in part, neither the validity of the
     remaining parts of such provision nor the validity of any other provision
     of this Agreement shall in any way be affected thereby. In lieu of such
     invalid, illegal, or unenforceable provision, this Agreement shall be
     automatically reformed and construed to include provisions as similar in
     terms to such invalid, illegal, or unenforceable provision as may be
     possible so as to be valid, legal, and enforceable.

27.  This Agreement may be executed in counterparts, and each counterpart shall
     have the same force and effect as an original and shall constitute an
     effective, binding agreement on the part of each of the undersigned.

IN WITNESS WHEREOF, intending to be legally bound, the parties have executed
this Agreement as of the day and year as set forth below.



Entrust Technologies Inc.          Paul Doscher

By: /s/ Jeff Bearrows              /s/ Paul Doscher
    -------------------------      --------------------------

Title:  VP, Human Resources        Date:  6/8/01
       ----------------------            --------------------

Date:  6/13/01
      -----------------------
<PAGE>

Schedule A
----------

--------------------------------------------------------------------------------
                             WARN Notice - Employee
--------------------------------------------------------------------------------



To:  Paul Doscher
Date:  6/4/2001
This notice of a:      [ ] plant closure    X mass layoff

is being provided to you in compliance with the federal WARN Act (Worker
Adjustment and Retraining Notification Act).  This information is based on the
best information currently available to us, but may change due to subsequent
events beyond our control.

Company Name:  Entrust Technologies Inc., also on behalf of enCommerce, Inc.
               -------------------------------------------------------------
Facility Address: 2901 Patrick Henry Dr., Santa Clara, CA.  95054
                  -----------------------------------------------

Expected date of closure/layoff:  6/4/2001
This action is expected to be                        X permanent  [ ]  temporary
If temporary, the expected duration of this action is
                                                     ---------------------------
The entire plant               [ ] will be closed    X will not be closed
Expected date of your separation __/__/__
Bumping rights                 [ ] do exist          X do not exist
For further information contact:        Stephanie Forrester
                                        -------------------
                                        (company representative)
                                        at:  (408) 222-7928
                                        (telephone number)



Dislocated worker assistance may be available to you through California's
Employment Development Department (EDD).  To locate the Service Delivery Area
serving you, call 916.654.7799, or contact your local EDD office.