How to lap a Heatsink
First the question of why?
Most heatsinks have a relatively rough base after their machining process (this is where thermal grease comes in). Even though it may feel smooth and flat, there are microscopic peaks and valleys which impede the transfer of heat from the CPU to the heatsink.
Now obviously with a rough base, only as much as half the heatsink may be contacting the CPU; thermal grease can fill these pits, but it's another substance for the heat to transfer through and it's not as efficient.
So we lap the heatsink to make it smooth so you get the best possible contact between the heatsink and CPU for maximum cooling. There will always be peaks and valleys, but lapping changes Mt. Everest to a small hill. Thermal grease fills these micro-voids, but the smoother the better.
Lapping can be performed on any type of Heatsink/Waterblock with a base, it can be Aluminium or Copper, (or a combination) just remember Copper sands much much quicker than Aluminium so be careful, and patient with Aluminium! (Most lapping takes about an hour for a Well done job)
Now for the process:
You will need some Wet/Dry sandpaper, if your heatsink is really bad a sheet of 400grit and one sheet of 600grit, if its not to bad just a sheet of 600grit.
Start by placing the sandpaper on a FLAT surface (a uneven surface is just defeating the object of the task, glass is often a Good Surface) pour a mixture of Water and a FEW DROPS of Washing up liquid (stops it sticking) onto the paper.
Now grasping the heatsink place the bottom (obviously!!!) onto the sandpaper, and make circular motions about 10-15cm in diameter, (it will be difficult and the heatsink will stick at first but as you progress and the bottom layer of the machining rubs off it will glide over).
Remember to press will reasonable force, every 100 or so strokes rotate the heatsink 90 degrees to make sure of an even surface.
Also every once in a while when the sandpaper looks very orange or silvery (the Metal particles) flush the paper with more water + Washing up liquid, keep doing this until the bottom of the Heatsink is smooth (test by running your thumbnail over the bottom and see if you can feel any obvious lumps). When its smooth you're done!!
A few notes + pointers now:
1> If the heatsink is really uneven to begin with (as I said above) start with a lower grit (more coarse) then after a Good 15-20mins of lapping check to see if all those Horizontal lines on the bottom are gone, if they are proceed to the 600 grit paper.
2> You may if you wish use a higher grit than 600 to finish with, some people even go to a 2000grit (so fine it would only take the shine and not the paint off a Mercedes body work) however it isn't necessary to have it so smooth, 600grit will give a smooth enough surface, going to a higher grit may make it shinier but you certainly won't get a performance gain (this has been debated many times).
3> After you have finished you may wish to clean the heatsinks surface with some Isopropyl Alcohol, I prefer to use this as it evaporates, unlike polish because you don't want a layer of anything depleting your Heatsinks performance.
For copper use a anti-tarnish solution you can buy, Brass-O is a popular one. its very Good at getting dirt out and making the surface as smooth as possible.
4> After you're finished apply some AS3 (this is the best Thermal compound) to the CPU's core as per instructions on
www.arcticsilver.com and apply the Heatsink, you may be wondering why you're adding a Thermal compound if its another layer?
Well simply AS3 only fills the crefaces, if there aren't any it moves out the way, so make sure you apply an even thin coat on the CPU core, else it will be dripping down your core (Don't worry its not very dangerous (unlikely to get a short circuit) its just messy!)
You're done!
Good Luck,
M_N