When you are married to a nonresident alien, how you file your income taxes is your decision. The Internal Revenue Service grants you the ability to treat your spouse as a resident alien and file jointly or you can waive that provision and file separately. You are still married, however, and are not allowed to file under the single status. When you file without your spouse, your tax liability might be lower than if you file jointly, but you lose the option to claim important tax credits.