My wife owes a court ordered restitution that she has not paid, if I file married seperatley, can they take my refund. We live in California and she doesn't work so she won't be filling at all.

You can file separately if you want, but a better option would be to file joibt and submit Form 8379 to claim Injured Spouse Allocation.

That way, you get taxed at the best tax rate (joint) and probably end up paying nothing because your wife does not work.

If you want professional help filing, enail me at the email address in my profile.