After reading up on lapping CPUs and heatsinks I decided I would give it a go today. For those that don't know what lapping involves, it is using increasingly finer sandpaper to flatten and then polish to a shine the CPU (actually the heat dissipation cover that is glued on) and the corresponding heat sink used to cool it. I have been reading up on this and the engineer in me figured it had some merit and was worth trying. Anyone that is thinking of doing this needs to note that this process will void your CPU warranty.
The cost of doing this is minimal. I used 400, 600, 1,000 and 1,500 grit sandpaper I bought at an automotive parts store for around $12. After doing this I recommend using 400, 1,000 and 2,000 grit. It will save you $3-$4 by not having to buy one pack of paper. I took the paper and taped it to a glass table top to make sure the sanding surface was flat. Mark an "X" on each piece so you can better see the progress. Then I just started back and forth motions of 30 strokes then turned the CPU/heatsink 90 degrees and kept repeating. It helps to dust off the sandpaper every so often to allow it to keep sanding away the material better. Try not to breath the dust. A vacuum with a brush attachment works great for this. The entire process took anywhere from 1 to 1.5 hours. It isn't real difficult. You just need to pay attention because things can get boring after awhile. BTW, the CPU heat spreader is actually made of copper with a metallic coating. The coating needs to be completely ground off and it does make it easy to see the high and low points of the plate.
One thing that really surprised me was just how non-flat the CPU and heat sink were. Both were quite concave and It was obvious just how poor the contact between them must have been. This process was done on an Intel E6700 CPU and a very cheap ($10 cheap!) Masscool aluminum heat sink with a 90mm fan. Also, I overclock the heck out this CPU and run it at 3.51 ghz (2.67 ghz stock) with a 5% voltage increase. Before lapping the temperatures for the actual cores while under 100% load averaged around 58C-59C. After lapping the temps went to 53C-54C and should get a little better once the paste (Arctic Silver 5) has a chance to set in better. Overall, I am pretty pleased with the results. Especially considering I am using a $10 heat sink and fan.
I know this isn't for the faint of heart or for the non-overclockers but for a little time and $10 worth of sandpaper the results are worth the effort, IMO.