If you have a 1099-R, there is box 5 for the employee's basis. See About Form 1099-R, Distributions From Pensions, Annuities, Retirement or Profit-Sharing Plans.
That basis can be subtracted to reduce the taxable amount. The issuer may have done that for you already. You can e-file the return with no problem.
Each situation is unique. I recommend you run through the IRS How Do I File a Deceased Person program. It is very detailed and will tell you exactly what is best for your situation.
I am very sorry for your loss.
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