You could file an innocent or injured spouse form, depending on which is relevant in your case.
An innocent spouse filed a joint return but was unaware that their spouse deliberately under-reported their tax liability. By filing as an innocent spouse (Form 8857), s/he can be protected from additional taxes, penalties, and interest when the IRS later finds out about the unreported income.
In contrast, an injured spouse seeks to protect his or her share of the joint refund in case it gets seized or offset due to the other spouse's debts or unpaid obligations.
Please comment back (and let me know if you've already filed or not) if you need help with either of these forms.
