What materials are used for such a project? I understand the idea that regardless of quality manufacture, an OEM CPU heat-sink (in this case on an Intel BOXD945GCLF2 Atom 330 Intel 945GC Mini ITX Motherboard/CPU Combo) will not be a perfect flat surface. So the need to lap its surface is obvious to me.

However, would there be a reason to not lap the surface of a CPU? I have no idea. I have never lapped computer components and I do know that doing something that may seem innocent could destroy an electronic component (such as a static electricity discharge that cannot even be felt can damage an integrated circuit).

I feel that I will have to stick with the OEM CPU heat-sink as I have not found an aftermarket heat-sink for the Atom 330 processor. Given that the processor runs on such low power, it probably does not need much more than the OEM heat-sink.

On the other hand, the Northbridge is equipped with a heat-sink and fan from the factory. At the very least, I plan to lap that heat-sink and replace the fan with one of high quality and possibly a lower sound level.

So, am I making any big mistakes?

And, of course, what is a proper method for lapping surfaces in this application?
Coldsomewildpaddle: Thank you for clarifying the situation. What you say does make sense, especially as I do intend to run this bugger at stock speed and load. I just enjoy being a perfectionist.

However, what will others say? We shall see.