If you are more than 5 yrs in US, then you are supposed to pay both tax. We can only get refund within 5 years. However, we need to fill out below different form and send the concern office. They will normally mail check or RFE.

form 843 http://www.irs.gov/pub/irs-pdf/f843.pdf

form 8316 http://www.irs.gov/pub/irs-pdf/f8316.pdf

Employer do withholding tax as like regular employee either F1 or not.