I haven't posted in a while, so I'll give you the lowdown:
It's basically what Rav said, but I'll explain the procedure.
First get some wet/dry sandpaper. I would suggest starting at 400 grit and working your way up to 800 or 1000. You can find the higher grits above 600 at car part stores. If the base of your HS is really not flat, like mine was (ridges each 1mm deep), then start at 220.
Then get a container or bucket or whatever filled with water and ONE drop of dishwashing liquid (to ease the friction). Then get something flat like a sheet of glass (recommended) and lay it on a flat surface.
Take a permanent marker and draw a squiggly lin on the base of the HS. This help determine the trouble spots and lets you see your progress. Naturally, once all the marker is gone, you're done with that grit. Mark the base again and move up to the next grit level. After the first time, it will come off much faster and it should come off evenly.
Now, you're ready to start:
-Wet the sandpaper and lay it on your flat object.
-Take your heatsink and set it down at its starting point.
-Now take it and, applying pressure as evenly as possible over every part of the heatsink, push it forward.
-Pick it up, put it back down at its starting point, and push in the same direction again.
NEVER rotate the HS and push in ONLY one direction. Check the base periodically to monitor your progress.