Yes, you can start a return as Married Filing Separate (MFS). If you want to be able to view the return or print it, you will have to pay without filing, but you can still make changes after you pay. Once you are done with your mock MFS return, you can go to the My Info section and change your filing status, marriage status, and add your spouse. All of your previously entered information will have been saved and you will not have to re-enter.
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