Originally Posted by wsail
Thanks, that's done. How do you compensate for the lower heatsink surface?
If you're using a HSF with a clip-on retention mechanism, you have to lower the retention module by approximately the same amount of material that the IHS' height is. Thankfully, this is pretty easy to figure out in most cases.
If you take the HSF retention module (the plastic thing on which the clips are attached) off of the motherboard, you'll notice that there are four (one at each corner) "bumps" on the underside. Compare the removed IHS with these bumps, and you'll see it's an almost exact match. Sand these bumps away, and you lower the height of the HSF retention module as well. This will therefore maintain the correct contact pressure for the HSF.
If you have a bolt-down HSF (Thermaltake Big Typhoon, Thermalright Ultra 120/Ultra 120 Extreme, etc.), simply crank down the retention bolts until they can't turn anymore. Don't worry about crushing the exposed core die; these are ultra-resilient, and I've yet to see a crushed die. Do take care with the peripheral ICs surrounding the core, as these are very fragile. I protect these with strips of electrical tape, just as some protection.
I've attached some pictures to illustrate the point.
Hope this helps!