elcido :
I just cleaned my heatsink with rubbing alcohol and a non abrasive cloth, when I was done I noticed it had left hundreds of minor circular scratches (cleaning scratches) on the beautiful mirror finish. Will this affect heat dissipation? Should I lap the heatsink before I install it?
I doubt that you will have any problem.
The purpose of the thermal material is to get air out of those minor imperfections. Air is a poor conductor of heat.
A mirror surface looks nice, but does little good if the surfaces are uneven and do not mate well.
It is not that important.
You are more likely to cause a problem by trying to lap the surfaces and getting it uneven.
If, after all, you think you still have a problem after mounting the cooler, you can always try to fix it later.