File 1040 NR. Law requires any non-immigrant working in US (i.e., authoriazed work in F1 or H1 status) to file 1040 NR. By filing 1040NR, you will lose regular standard deduction provided in 1040 but you will be able to get your Social security and medicare tax. Consult a good tax preparer.... Tax software are not made for special situation like yours nor local H & R block. So, consult a good tax preparer who knows what he is doing.