I came to US in August 2003, finished my studies in May 2008 and started working full-time (OPT) from August 2008. Currently I am paying both SS and Medicare taxes. Do I have to pay these taxes as I am working in OPT and technically still under F1 visa? Or am I considered resident alien since I have been in US for 5 years?
Thanks,

On F1 you are exempt from residency for 5-years so from the sixth year you must pay SS and Medicare taxes.
You will file resident tax return in 2008.

Thanks for the reply. Since OPT has been extended to 29 months, any chances that the 5 year period also be extended? And will I get refund for SS and medicare taxes?

You CAN avoid paying Social Security and Medicare taxes by filing Form 1040NR and 8843 for 2008 AND submit proof that you are maintaining a "closer connection" with your home country.

Burden of proof for this closer connection is on you, and if you apply for a H-1B visa, that action will disallow any claim for closer connection.

I agree that you may be able to claim nonresident status, but that the burden of the closer connection to your home country is on you. If you apply for a green card, then you likely will not be successful in arguing that you are temporarily present in the U.S. The regulations do not identify such a bright-line test for applying for a H1-B visa.