The thermal paste is what is used to cover over these imperfections so you get good mating of the surfaces. because you are serious about what to do I am adding the article I had found for you.
Lapping: Smooth as you Wanna Be
The machining process used to manufactore most heatsinks often leaves their mating surfaces rough and covered with tiny pits and valleys that can trap heat. It is because of these imperfections that we use thermal compound between the CPU and the heatsink to ensure the best heat energy transfer possible between two uneven surfaces. Ideally, mating two perfectly flat surfaces together would require no thermal compound whatsoever for good heat transfer.
Fortunately, there is an inexpensive, simple method called "lapping" that will help you remove imperfections on the surface of your heatsink and CPU. You will need a small list of supplies, including a pack of automotive-grade wet/dry sandpaper (220grit through 600-grit), a black permanent marker, some water, a tube of abrasive rubbing compound, a flat piece of glass (or mirrored glass), and some towels or rags (clean).
Because we are striving for a surface that is as close to flat as possible, you will need a flat surface to hold the sandpaper during the lapping process. First arrange one of your towels or rags flat on a sturdy surface or countertop, and thengently place you mirror or glass on top of this. the towel will help ease the stress between the countertop and the glass itself at the same time the towel helps catch the water runoff during the lapping process.
Take your permanent marker and graw several lines across the face of both the CPU and the heatsink. These lines will act as guides that give you some idea of just how uneven these surfaces are. Starting with the courses sandpaper you have (220 grit), place a small amount of water in the middle of the sandpaper, apply even pressure, and work the heatsink back and forth. Check the surface of your heatsink often during the lapping process to monitor progress. Once the high spots on the mating surface are removed (most of the lines from the permanent marker will be gone), you can switch to a finer grade of sandpaper (400 grit). Using a small amount of water, repeat the sanding process until you are ready to move to the finest grade sandpaper (600 grit). Repeat this process on your CPU. to avoid damage to the pins on your CPU, make sure you leave the CPU in the socket type holder your process was shipped in. if you are in need of something to hold your CPU and protect the pins, I suggest some stiff foam or a small piece of styrofoam that you can gently push the processor into to avoiding bending or breaking the CPU pins while lapping the mating surface.
Once you have completed the sanding process od lapping your CPU, you can use the heavy grit polish or rubbing compound to finish off your mating surfaces.If the whole process of lapping your heatsink has not dissuaded you yet, there is an extra step, a method I personally use called "match lapping" that might interest you. Match lapping consist of carefully lining up the heatsink and CPU just as the would when they would be installed, put a small amoutn of abrasive compound between the heatsink and CPU, and working the processor back and forth in small strokes. This process is essentially a final polishing process that mates the face of the CPU with the contact area of the heatsink.
Under no circumstances should you hold the sandpaper with your hand while lapping your heatsink or CPU. The uneven pressure of your fingers will cause ruts and make a rough, porous surface even worse.
This was taken out of CPU's spring 2004 edition of PC Modder Mag.and was most likely wrote by STEVE LYNCH
My take is this, if yor the type of person thats like as close to perfection as can be had and like spending time on the small minor details that can make all of the difference in the world, then go this route. On the other hand, if you just cannot wait to get that Computer back up and running, just spread the thermal paste on that sucker and go with it (heck you can always take it back down a do it right later).
Hope this helps you out since it took me thirty minutes to type.