No. The IRS will not permit a couple to amend and change their filing status to married filing separate. However, if your tax refund was taken by the taxing authority and you had income in 2016 then you can file an injured spouse form to get your portion of the refund.
You can file an injured spouse claim up to three years after the due date of a return See the following from IRS Form 8379 instructions:
Follow the instructions below if you qualify to file an injured spouse form.
- Click on Federal Taxes (Personal using Home and Business)
- Click on Other Tax Situations
- Scroll down to Other Tax Forms
- On Miscellaneous Tax Forms, click the start or update button
- On Report an innocent or injured spouse claim, click the start or update button
Alternatively, type in injured spouse in the Search box in the upper right of the program screen. Click on Jump to injured spouse
Note: If your spouse just owed money last year because not enough tax was withheld, then you cannot file an injured spouse form.