For optimal heat transfer the contact point between your CPU core and the heatsink should be both smooth, flat and clean. If the surface is not smooth enough you can always
lap it to reduce the imperfections on its surface, but for cleaning, we often get asked just what cleaners to use, how to clean the chip, and how safe it is to clean the chip using various methods.
Clean the surfaces of the chip die or core using a solvent such as high-purity isopropyl alcohol or an acetone. Both of these are available at a pharmacy, druge store, super market, or hobby shop. First apply the solvent on a lint free cloth or the tip of a Q-tip and use that cloth or q-tip to swap or wipe the core. People keep asking what a LINT FREE cloth is... basically any cloth designed not to leave any lint behind or pick up and drag any abbrasive solids - eye glass or photography lens cloths are good examples. If you're using acetone as a cleaner you might need to wipe it off with isopropyl alcohol after because acetone has a slick quality about it.
To clean the ceramic surface of an AMD Athlon and Athlon XP CPU (that's the reddish-brown area around the CPU core) you can use dish detergent, isopropyl alcohol, or a citrus based cleaner. Apply using q-tips if you are having trouble with getting between components. Don't use mineral spirits here though just in case you get it on the core. Modern P4 and Athlon64 chips have a heat spreader that cover the ceramic - the spreader can be cleaned just like a CPU core.
For basic cleaning jobs on the heatsink you can use isopropyl alcohol or acetone again, however a product like Goof Off, carburator cleaners, or mineral spirits (or even super high 99% pure isopropyl alcohol) might be more effective. If you have some old thermal paste, thermal pad, or thermal putty left over on the heatsink you probably have to use the latter products just to get a good cleaning. If you use something like the mineral spirits or carburator cleaner wipe down the heatsink with isopropyl alcohol when you're done. For the heatsink you can clean using paper towels instead of using a lint free cloth. Facial tissue or bathroom tissue will leave behind lint so we recommend avoiding it.
When cleaning your CPU or heatsink we recommend you start out by cleaning your hands or using a pair of plastic gloves. If you do use gloves, make sure you're using the clear plastic disposable gloves that you can get at a superstore (the ones used for stuffing turkeys and reading newspapers) and NOT the surgical gloves used in labs and hospitals - these latter gloves have a layer of powder that would be an additinal impurity on your heatsink/cpu. If you don't use gloves, clean your hands using dish detergent like Dawn or Palmolive - these are good enough to strip away some oils but not leave some sort of nutrient or chemical residue. (in other words, don't use soaps like Dove or moisturizer soaps or dish washing machine detergent).
Cleaning your CPU/heatsink is an important step during the installation of your CPU/heatsink. Contaminants like old, dried, or less effective thermal paste or finger oils can reduce the effectiveness of your new paste. Lint, hair and dust can reduce surface contact and adversely affect heat transfer. Remember, on some CPUs the contact surface is only the size of a your fingertip, so the contact between surface areas is extremely important.
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