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Optics cleaning gives a lot of general guidelines on cleaning, consider consulting a textbook for more detail.
Popular cleaning agents include:
Acetone bath + ultrasonic cleaning (ultrasound) are effective to remove latent debris and generally is the preferred workhouse method in a professional setup. If ultrasound is not available, first try pressurized solvent from a squirt bottle or pipette. If this does not remove debris
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The most extreme contamination you are likely to encounter is from grinding a TO-3 or similar open:
After blowing off you'll still have massive contamination:
Washing with water followed by acetone will help considerably (sample picture taken while still covered with acetone which is somewhat cheating since it makes it look better):
But there are still a lot of particles. These can be brought down much lower still by ultrasound:
Above was taken after 8 minutes (Beck indicates 1 minute should be sufficient, did not take multiple pictures to show length effect) ultrasound, water wash, and then acetone wash. If the sample was needed really clean it could be put through another run. Of course normal washing will continue to improve the sample as well, but *much* slower.
A good starting cleaning technique since its inexpensive, quick, and may even be sufficient for final analysis depending on how decapsulation was done. Use a syringe or small tip pipette to shoot a jet of solvent at the die.
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Uses techniques similar to those for cleaning optics.
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Use a mild abrasive (ex: toothpaste) as a buffer to apply force to die surface.
Generally an acetone rinse should take care of dust.
Can be blown off with a sufficiently clean air supply but generally these are hard to come by. For example, optics cleaning tends to recommend against using compressed air cans. They said that if you insist you must use them upside down to allow particulates to settle and must spray for a bit elsewhere first to clear out the system.
After epoxy decapsulation the chip may have bits of epoxy still hanging around. Sonicating in acetone should clear it up with most epoxies. I've found a few compositions that don't but I'm not clear on what the difference is. In these instances pressurized acetone from a syringe tended to work well. This is also a good method to remove hard to take off grit that acetone will not get. If you are still having issues considering briefly soaking in clean RFNA or hot clean H2SO4 as the epoxy might not be fully dissolved.
After decapsulation the sample will have traces of acid on it that will likely corrode it over time. Use the standard procedures discussed on the epoxy decapsulation pages: acetone wash to remove bulk acid, soap and water for a deeper clean and to remove salts, and finally an acetone wash to dehydrate the chip.
Shame on you if you picked up a die with your bare hands but things do happen. Acetone does not clean off fingerprints very well but soapy water does. The above picture was taken after putting a fingerprint on a slide and sonicating in acetone for a few minutes. It has little to no effect. Fingerprint oils do not respond to polarized light (ie will black out).