My spouse is neither a U.S. citizen nor a U.S. resident. My tax returns ‘married filing separately’ was rejected as IRS. What correction I do to file this again?

If she doesn't have a Social Security number or an Individual Taxpayer Identification Number (ITIN), you won't be able to electronically file the return. You will have to mail your return.  

If you wanted to file as married filing joint, you could apply for an ITIN, for her.  To do this complete IRS Form W-7, IRS Application for Individual Taxpayer Identification Number. Form W-7 requires documentation substantiating foreign/alien status and true identity.