The best way to clean thermal paste off a CPU is to use isopropyl alcohol (as high a percent as possible like 90%) and a coffee filter. Using something like Q-tips or tissues can leave behind small hairs or fibers. Coffee filters leave nothing behind. Get the coffee filter damp with solution and wipe the thermal paste. Alcohol prep pads (for site injections) can be used as well. They are convenient and perfectly sized.
If you are having a tough time cleaning the thermal paste from a CPU, try using fingernail polish remover and a Q-tip. The fingernail polish remover should be the basic acetone kind with no additives or fragrances. Once you have cleaned the thermal paste off a CPU, wipe the area with the isopropyl alcohol and coffee filter, or with the alcohol prep pad. Dry the area with a quick spray of canned air which will dry any dampness and blow away any fibers that may be left from the Q-tip. And that is how to clean thermal paste off a CPU.