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CPU damaged?

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I had recently cleaned my CPU of thermal paste because I was installing an H100 cooler and I noticed on the top of the CPU that there are 2 spots that feel like tiny tiny holes the size of the tip of like a paper clip. You could barely notice them but I was wondering if it could become a problem? I always touch the CPU by the edges and I've never touched the top except for cleaning it. I had gotten it about 2 weeks ago. Is it also possible that it could be hardened/dried up thermal paste that is really just stuck and hardened to the CPU from the stock cooler I had on it?

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Just worried because I had just bought it and I thought it was cracks or something. : /
I was also told that I should just remove all of the old T.I.M. I don't know how to and it doesn't seem necessary.
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you should clean old paste to get a good connection with no air between surfaces . 97% ISOPRopyol alcool , I use Goo Gone then clean that with eye wash with .03% boric acid , not sure others would use my method but it's worked for over 100 cooler install changes . And use a lint free cloth or coffee filters

I can't really take a pic because I'm currently using it and I doubt my camera would pick it up but I haven't had any problems. I actually was just running some stress tests and my temps are fine. Lets just say it looks like a dirt spot and it feels smooth when you slide your finger across it. It's pretty centered and I had noticed it when cleaning it. If I were to slide the tip of my nail across it you would somewhat feel it. Also, I cleaned it with q-tips, rubbing alcohol and coffee filters.
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