If you are required by law to electronically file all of your clients' tax returns, but need an exception to this requirement for a particular return, you should file IRS Form 8948 Preparer Explanation for Not Filing Electronically. This form is available in the TaxAct Professional Edition of the software and is accessed through the Forms View.
Per the form instructions:
Attach this form to the paper tax return you prepare and furnish to the taxpayer for the taxpayer's signature. File Form 8948 with the tax return that is filed on paper.
Form 8948 is used only by specified tax return preparers (defined below) to explain why a particular return is being filed on paper. A specified tax return preparer may be required by law to electronically file (e-file) certain covered returns (defined below). There are exceptions to this requirement, and Form 8948 is used by specified tax return preparers to identify returns that meet allowable exceptions.
A specified tax return preparer is a tax return preparer, as identified in section 7701(a)(36) and Regulations section 301.7701-15, who is a preparer of covered returns and who reasonably expects (if the preparer is a member of a firm, the firm's members in the aggregate reasonably expect) to file 11 or more covered returns during a calendar year.
Aggregate Filing of Returns. For the e-file requirement, "aggregate" means the total number of covered returns reasonably expected to be filed by the firm as a whole. For example, if a firm has 2 preparers and each preparer in the firm reasonably expects to prepare and file 6 covered returns, the aggregate for the firm equals 12 covered returns, and each preparer is a specified tax return preparer.
Additional information can be found on the IRS website Most Tax Return Preparers Must Use IRS e-file.