If you want to ensure real flatness there is only one way:
1. Coat the entire bottom of the heatsink(machinists use a special colored dye, you could use magic marker).
2. On a large FLAT surface(a piece of glass or a mirror are usually readily availed in the home) place a piece of very fine grit sandpaper.
3. Apply even pressure to the heatsink while you gently sand it in a figure-8 pattern.
You will notice spots where the dye or magic marker have been removed and spots where it has not. The uncolored spots are high spots.
4. Repeat steps 1-3 until you see no more highspots
This is called lapping, it will ensure a flat level surface.