I filed married and separate. I put his name and ssn on the form. When he filed the it rejected saying his ssn was already used. Do I need to amend and remove ssn?

No, when you file separately, you still include your spouses name and ssn. It's possible he has been a victim of identity theft.

 

Unfortunately the only option will be to paper file. I would also suggest he Complete IRS Form 14039, Identity Theft Affidavit and mail it along with his return.

 

More information can be found here:

Identity Theft Guide