I have been on F-1 for more than five years (since 2002) which means that I am considered a resident alien for tax purposes. However, no FICA taxes were deducted from my paycheck. My status changed to H-1B on Oct 1, 2008. Again, no FICA taxes were deducted. Any solution? I read that I could use form 4317 to report Medicare and Social Security taxes. However, box 3 of my W-2 (Social Security wages) and box 5 (Medicare wages) are blank. I am confused. How do I report/pay the taxes?

You must go to your employer and explain that these taxes should have been paid. Do this to at least start the withholding, and do it in writing (email is good for this).

Once you have so notified the employer of the oversight, you need to let the employer handle it from there. You cannot pay these taxes independently; they MUST be paid through the employer.