Hi,

I was on F1 visa whole of 2006 and 2007. I filed my taxes for 2006 and 2007 as Resident.
Later I figured out that I should have filed it as Non Resident.
Should I file an amendment for correcting it? Or is it fine to leave it as is?

Since I was on F1 the place where I interned did not detect any Social Security Taxes or Medicare.

On the resident return, you are required to pay FICA taxes.
What is current visa and your status in 2008?

My H1-B started this October 2008...
I am paying FICA taxes from oct 2008. Before that I did not pay any...

Your FICA situation is correct.

You need to amend your 2006 and 2007 returns with Form 1040X, attaching a correctly-prepared Form 1040NR to each 1040X submitted, plus Form 8843,

For 2008, you file Forms 1040NR and 8843 one last time.