Hi,

I was on F-1 student visa during 2009. I spent 3 months on CPT and both social security and Medicare taxes were withheld from my wage (about $1300) during this period (which I believe I was not subject to these taxes as nonresident alien).

Now, when I do my 2009 tax, I owe $1100, I completed form 8316 and843 for claim these taxes. My question is, should I pay the $1100 to IRS and wait until they refund those erroneously withheld taxes or there is a way to put these numbers in my 1040-NR form and wait for $200 refund? (Honestly I don't have $1100 now :) )

Thanks!

Form 843 is not filed with your tax return. So file tax return and pay the tax due or pay what ever you can with the tax return
Wait for one month, and then file Form 843.