A coffee filter works great on the final passes. Lens paper is another good/better choice. Reduces the lint factor. You want no lint at all. No fingerprints, water drops, oils, lint, nothing but pure surface-paste-surface.
When you want to remove the thermal pad on the heat sink, you might want to consider a "scraper" of sorts to CAREFULLY push the bulk of it off and follow with a good cleaning using a filter or lens paper. DO NOT scratch the surface so be careful with that method.
Back in the day, I used to hand lap the heat sinks on extremely fine wet sand paper immersed in water on a flat piece of glass. Following with a light tinting is still a good idea.
A good guide to read:
http://www.arcticsilver.com/intel_application_method.html#Good looking build, "Gootch"!