Thanks kale bhale.. This makes my confusion a little bit clear. But if I file as single and since I am married and the USCIS has all of my information, won't they see me as a fraud. Being married and filing as a single. And even if I file as a married filing separately they still ask for the spouse's SSN or ITIN. So it means I need to file 1040 NR like kale bhale said. Ok then I will go ahead and file 1040 NR. Thanks again for everybody!