I was freelancing for a company on my OPT from August 2008 to September 2008, and then was hired full time at another company from October 2008. Social Security and Medicare were deducted, and I filed my taxes using TurboTax, not knowing I'm eligible for the exception. From Jan 2009, I became a resident alien since it's been 5 years of my stay in US. Since it's been over a year and the taxes have been filed, should I still need to ask my employer for refund? Because that be only partial refund and does not cover the taxes I paid on my freelance earnings, or should I fill the 843 and write to IRS for the refund?

Since you file resident return for 2008, you will not get refund of FICA taxes.

Thanks for answering my question