How do I file taxes with a non resident spouse who is self employed?

It depends on if you want to file a joint or separate return. If you want to file a separate return, all you need to do is print and mail your return writing NRA and your spouses name on the spot that asks for your spouses name, unless they have an ITIN.  If they do, then you can e-file your return.  You would not include anything of their income on your return. Their income would not be taxed by the IRS. 

If you want to file a joint return, then you will report their income in the Less Common Income section as Foreign Earned Income and Exclusions. If you file a joint return, all of their income from worldwide is taxed as if they are a resident of the US.  If they already have an ITIN, then you would just need to enter it and continue. If they do not, you will need to print and mail your return along with the W-7 and any other required documents to

IRS

ITIN Operation

P.O. Box 149342

Austin, TX 78714-9342