In response to Wolf's PM: You do
not want to rotate the heatsink 90 degrees. Many people will tell you to, and many guides on the internet will tell you to, but this will cause the bottom of the heatsink to not be flat. That's not good.
I would lap with only 600 grit, but if you really want to go higher then I guess 800 grit would be fine. I would not go any higher than that. Lap until you are satisfied with the smoothness basically. Sometimes when you get a heatsink there are visible dents, ridges, or markings on the base and these are what lapping is intended to remove; sometimes you can even run your fingernail across the base of the heatsink and feel ridges from when the saw blade cut the metal.
A good way to gauge how much to lap is to color the bottom of the heatsink with a permanent marker... When lapping you can look at the bottom to see if you are applying even pressure and how much of the base you have sanded off. Once all of the marker is gone your base should be flat unless there were severe dents in it to start with.
Keep in mind that the marker on the front edge of the heatsink will wear off first, but this is intended - if you see this do NOT rotate the heatsink or then you will give your heatsink a convex base. When you sand anything, no matter what method you use, the front edge of the material you are lapping will always get the most sanding. If you use a circular or figure eight motion then this means that all edges of the heatsink will be the front edge through the motion, and the middle will be the only area that benefits less from the sanding - hence the convex base. If you use the straight method, then there is only one front edge and the base of your heatsink will remain flat, though it will have a slight slope.
Here is the important part: With heatsinks, it is better for heatsink to die contact if you have a flat slope than if you have a convex surface. It only makes sense.
Here is some more information on lapping from a couple people who have the experience and resources to accurately comment on this topic:
follow the procedure that Greystar described above
its the same that I use
one direction, lift and return - never rotate
close to impossible to actually get it flat by hand, I never have
(and I can, and do, inspect for such)
be cool
Like Dago basically said though, to each his own... You gotta do what your comfortable with.