You lap the heatsink...it's the easy one.
Some people do lap the suface of the GPU or CPU, but it's more difficult.
Find a flat surface like a good kitchen counter or some thing similar and place a pane of glass on it (maybe 8 in x10 in). A sheet of newspaper under the glass would help avoid scratches to the counter.
Get 2 grits of sand paper, maybe a 200 and 600 grit in full size sheets.
Place the sandpaper rough side up on the glass and sand away to your desired finish.