In the interest of a better thermal connection between the heat sink and the case, wouldn’t it be better to remove the anodisation on the contact surface of the case?
Google AI says, in response to “anodized aluminum heat transfer”:
Anodized aluminum is more effective at releasing heat than unfinished aluminum because of its higher surface area, which improves its thermal conductivity and emissivity.
Improved thermal conductivity
The oxide layer formed by anodizing aluminum alloys improves their heat dissipation performance.
Also a lot of commercial heat sinks are anodized, and they don’t remove it unless they want electrical conduction also.
Indeed, due to the increased surface area of anodized surface there is an increase in thermal radiation and convection but I believe there is a reduction in thermal conduction which is what is required to conduct the heat from the heatsink (thermal block) to the case. We want the heat to conduct from the microprocessor to the thermal block and then to the case which can then disipate the heat into the air via radiation and convection. So the minimum resistance to thermal conduction between the microprocessor and the heatsink, and between the heatsink and the metal enclosure is optimal. Then maximising the surface area of the outside of the metal enclosure is beheficial.
So the optimal heat exchange comes with no anodisation on the heatsink or case surface that mates with the heatsink but anodisation on the outside of the case. It is not clear how much thermal resistance is introduced by the anodisation so it may be of limited benefit to remove it from the inside of the case, but @jofemodo may want to consider if there is a benefit in masking that area of the case during fabrication.
It is also not clear whether oxidation has more or less impact on thermal conduction than anodisation. If oxidisation had a significant negative impact on conduction, then it would be important to remove oxidisation before fitting the heatsink, e.g. lightly sanding with abrasive paper.
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As @riban already wrote, I’m with you if it comes to dissipation. But at this specific point we need maximum thermal flow from heat sink to case (which then indeed is ok to have the additional surface through anodisation to get rid of the heat).
If it comes to heat sinks I have many high performance CPU heat sinks in mind, which regularly come with a plain, unprocessed contact surface to maximise the contact area and therefore the thermal flow. As I understand it, the anodisation acts more as a resistance here.
If I’m thinking about it, the optimum from my point of view would be a masking of the heat sink contact area during the anodisation process and then (dipending of oxidation of this area meanwhile) have some sanding or alcohol (on the surface, not intake! 
) before installing the heat sink.
But I’m not a specialist in Materials Science, so if anyone wants to add his views?
Reference:
From Anodizing - Wikipedia
“Anodized coatings have a much lower thermal conductivity and coefficient of linear expansion than aluminium.”
I am 
Anodizing is done for two reasons:
1 - as protection against oxidation of the aluminum alloy - or corrosion, let’s imagine it as oxidation with subsequent possible layer falling off or similar unpleasantness. Aluminum oxides are usually gray and sticky to the touch.
2 - better appearance (colors) , you won’t leave so many visible fingerprints on this surface
The anodized layer is thin, so it doesn’t affect the thermal properties that much.
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Masking the contact area will increase costs without improving things significantly.
Anodized thickness is just a few micrometers, so the overall effect on thermal conduction is negligible for most applications.
In our case, the “surface finishing” process improves thermal conduction because “sand blasting” increases the exposed contact surface with the thermal pad and “anodizing” prevents raw aluminum gets oxidized in the period from manufacturing to assembling.
Note that removing the oxide after will be difficult, precisely because of the sand-blasting process, so we should add a protective sheet to avoid it, etc.
Current solution works really well and adding complexity for improving by a 1% is not worth the effort.
Thanks!
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will void the guarantee
ok, I’ll …
