I'm a Japanese. I was working on F-1 OPT. I was with an agency and paying tax. But I had to change agencies because the company decided to cut all the temps. With the new agency, I was getting full amount(no tax deduction); namely I was self-employed but still working at the same company doing the same things. I'm already in Japan but I asked a tax accountant to do my tax before I left. She says I'm getting almost full tax return for the tax I paid when I was with the first agency, but I have to pay full tax for the amount I got from the 2nd agency. On OPT, Med and SS are exempt, and Federal is returned. But do I have to pay the full tax because I was self-employed? Was I working illegally in the first place?

On F1/OPT you are exempt from residency for 5-years. You must file non-resident tax return Form 1040NR or 1040NR-EZ and Form 8843. Your income is not subject to FICA taxes but you must pay federal and state income taxes. You will not pay SE tax. On your income you will get deduction based on tax treaty between the U.S. and your country. Your U.S. Tax Return: U.S. Tax Filing Requirements for Non-Residents