alright... here's how you do it:
first get a piece of glass, a tile or anything that is extremely flat. It has to be flat or it won't work.
then get yourself some wet/dry sandpaper. you want several grits... I have 600, 800, 1000, 1500 and 2000. you can get it from an automotive store
you want to tape the sandpaper to your piece of glass w/ masking tape... and get the sand paper wet. some people use water, or a dish soap. you can also use a window cleaner or buy a special lapping liquid stuff.
so you want to hold your heat sink firmly and go back and forth with it on the sandpaper... several times... keep track (I usually do about 60) then rotate it 90 degrees and do it again... keep this up till you've gone all the way around. when you're done you can do it again or go to the next finer sand paper. keep this up till you've got to the 2000 grit and you can see yourself in the base like a mirror.
at this point there are varing philosophies... some say use rubbing compound to get that 'mirror' finish, while others say no, because then you leave some rubbing compount residue and it interfere's with heat transfer... thermal compound is the only thing that's supposed to be bt/wn the cpu and the heatsink. I don't use rubbing compound... but this step is up to you.
that's it. you're done.
if you are still unsure you can buy a lapping kit from frozencpu.com. it costs a bit more, but you get the grits you need and directions. This is what I did because I wasn't sure... the only problem is that I ended up going out and buying sandpaper anyway because the one sheet of each wasn't enough. My Big Typhoon's base wasn't very smooth to begin with.
Here's a couple pics of what it should look like when you're done. Now, remember I didn't use a rubbing compound so I didn't achieve a complete mirror surface... you can see tiny scratches in the base, but it is much better than it was originally... my roughly 6 hours dropped my temps a couple degrees.