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 are unable file your return electronically because the primary and/or secondary SSN was misused, attach this form and documentation to your paper return and submit 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.