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I have long seen people recommending heatsinks to be as smooth as possible for optimal thermal transfer from the CPU to the heatsink. It’s explained that the smoother it is, the more contact there is between the two metals and avoids tiny cracks or scratches which can fill with (thermally insulating) air or worse, thermal compound which actually backfires when used in excess. I have even seen guides on manually polishing the heck out of them to a mirror finish.

If this is the case, then why is it that CPU covers usually come in brushed metal—there are plenty of visible (usually parallel-ish) lines/scratches on them. Worse, the make/model/speed/etc. are engraved in the metal. They often even have a little hole in one corner; what purpose that serves is beyond me. Isn’t it bad when it gets clogged with thermal paste?

Don’t all these defeat the purpose of a nice, smooth surface? Don’t they reduce thermal transfer and thus increase the operating temperature of the CPU? (Perhaps the effects of lapping are too little to bother with, so CPU manufacturers don’t care?)

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You'd typically join the heatsink to the CPU casing using a thermally conductive adhesive. The adhesive will fill in the cracks and create a completely consistent surface for the heatsink to bond to if it's applied correctly. The slightly rough surface may (I do say may here, speculative on my part) even be necessary for the adhesive to find purchase on the case.

Ultimately the there's spaces in every material at the atomic level. Huge spaces really. This is definitely a bit of spacing I wouldn't sweat too much.

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Well, at the atomic level, you’re not going to get air molecules or thermal paste stuck in between the metal atoms. –  Synetech Jun 12 '11 at 1:25

Watch out for post-decisional dissonance. Simply putting effort into something can convince a person that the idea was a good one. The more the effort, the harder it is to admit that it was pointless or counter-productive. A long time polishing the heatsink, without a resulting disaster, and people will tend to "see" a subjective difference in cooling performance whether there's a real difference or not.

Similarly, I have put some effort into the following answer - but I have no objective evidence to back it up...

The higher the surface area, the quicker the heat transfer - a brushed-metal finish is a good idea in that sense. Taken to a too-rough excess, you can't make a good contact between the two surfaces, but that doesn't mean a mirror finish is optimal. AFAIK, the manufacturers deliberately create that lightly brushed surface - it seems unlikely that they'd go to that trouble if there were no point, or if it damaged heat transfer.

When you buy a chip, the stock cooler often has thermal compound pre-applied. There's not a huge amount, but it does evenly cover the whole surface, and is plenty enough to cope with the lightly brushed metal that it coats.

I can't say for certain, but my guess is that polishing the surface is a slightly bad idea.

Worst case I can imagine - if you manage to polish the surface so that it's not quite perfectly flat (you're likely to polish the middle more than the edges), you might just manage to create an air bubble between the two surfaces.

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Hmm, wouldn’t the slight air bubble be filled with thermal paste? Now that you mention it, I don’t recall if you apply thermal compound at all if you lap them; I suppose it might defeat the purpose. –  Synetech Jun 12 '11 at 1:26
    
@Synetech - in reality yes, but my absurd point is that you might just manage to trap the air in. The thermal paste will still try to fill the gap under pressure, but since the air has nowhere to go... Anyway, if there's no thermal compound, a brushed surface is definitely a bad idea (it can only reduce the contact area) - but no thermal compound seems like a bad idea anyway. –  Steve314 Jun 12 '11 at 15:55
    
So I suppose that a slightly scarred surface doesn’t matter when using a thin thermal compound layer because it fills the tiny gaps (obviously you don’t want thick globs of compound). And as Ian said, the light abrasiveness of the surface could hold the compound in place (I find that AMD/Intel usually ship with a thermal sheet as opposed to paste). –  Synetech Jun 12 '11 at 16:36

Just like lapping can improve your temps (by 1-10°C), so does engraving have a small effect.
The thicker the thermal paste the higher the temperature, we are speaking about small differences though...

I have seen people run there computer without thermal paste with lower temps, you need good grit for that.
I think the effect of the engravings is minimal, resulting in a < 1°C difference

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“true grit”? :-D –  Synetech Jun 12 '11 at 1:23
    
@ Synetech inc, lol. –  Moab Jun 12 '11 at 13:30

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