After you file

If your tax returns for those tax years have already been filed and accepted by the IRS, then you can only amend the tax returns.  You cannot just re-file as originals.  
Each tax year would require you to complete an IRS Form 1040X, Amended U.S. Individual Income Tax Return.  A federal amended tax return, Form 1040X, can only be printed and mailed, it cannot be e-filed.

Additionally, since you paid the CPA for completing those tax years, then the CPA should file an amended tax returns for you.