Hi ashoksagar. The kernel creates modversions.h. There are a couple of things to do. First, put a clean kernel source (one that has never been used) into /usr/src/.
Next, do updatedb. This is important to enable your kernel compile to find everything.
Then log in as root. Don't use su & a password. Log out of your usual wm and log back in as root. Then compile your clean kernel source.
This is the sum of advice that was given to me, and it worked. Hope it helps you too.