After installing a Ryzen 5 5600X3D, I noticed unusually high temperatures: around 90°C during games at 60–70% utilization, despite using a Noctua NH-U12S cooler and running the fans at full speed. Removing the cooler revealed a small piece of metal trapped between the cooler and the CPU's integrated heat spreader. I removed the debris, but it left a gouge and raised burr in the IHS. The damaged spot catches on a fingernail or the edge of a credit card.
I lightly used rough sandpaper and remounted the cooler, which improved temperatures somewhat, but gaming temperatures are still around 75–85°C with spikes to 90°C at roughly 55 watts. I'd like to flatten the damaged area while removing as little metal as possible. Since the gouge appears to be near, but not directly over, a CCD, would filling it with thermal paste be sufficient? Should I use finer sandpaper, a diamond file, or another method?
3 Answers
A machinist’s stone or fine abrasive paper attached to a flat sheet of glass would be more controlled than freehand sanding. In this case, though, the goal should only be to knock down anything protruding above the IHS—not to aggressively thin or reshape the entire heat spreader. If you have access to a small machine shop, someone experienced could remove the burr quickly and evenly.
You can lap the integrated heat spreader, but it is a risky and fairly irreversible repair. The usual method is to secure fine sandpaper to a genuinely flat surface, such as glass, and move the CPU evenly across it, progressing to finer grits. This can remove the burr and flatten the surface, but it may erase the markings and reduce the CPU’s resale value. Avoid using a file unless you only need to remove a clearly raised fragment, since it is easy to create a larger uneven area.
If no part of the gouge is raised above the rest of the heat spreader, the safest option is probably to leave it alone. Apply thermal paste so the depression is filled and avoid trapping an air pocket. A small defect away from the die usually has very little effect on heat transfer.
If there is a burr sticking up, carefully remove only that raised material with very fine abrasive paper, then clean the surface with isopropyl alcohol. Before doing more work, also double-check cooler mounting pressure, thermal-paste coverage, and ambient temperatures—the damage may not be the real cause of the high temperatures.

That would be my first approach too. A shallow defect in a non-critical area is unlikely to explain those temperatures by itself.