Taxpayers who may have been victims of identity theft are still expected to file a return. Instructions for doing so are listed at IRS.gov and outlined in Form 14039.
The IRS instructions for Form 14039 state:
If you cannot file your return electronically because the primary and/or secondary SSN was misused, attach this form and documentation to your paper return and submit it to the IRS location where you normally file.
For more information, see IRS Form 14039: http://www.irs.gov/pub/irs-pdf/f14039.pdf
This information applies to all years of the UltimateTax software.