Lapping by hand is imprecise, but still better than a convex base. I didn't have time to try machining the base properly, but went with the hand method, using diamond-coated files that I use on guitar repairs/builds (that are flat enough for the purpose), then finished up with sandpaper (I only had up to 400 grit) on a flat metal plate (glass will work, too), and then polishing compound to at least smooth things out some. The idea is go to slowly, stay accurate, and prevent the base from being convex again, or from being tilted.
A good, flat, knife-sharpening block will also work well. With such a large cooler, it's easy to reconvex the base, so inverting it (fins down) will help. I had mine slowly spinning while I used the file, and it made a starburst, or asterisk type of pattern overall (though it was constantly turning). The base did have a small ridge that was more like this symbol: /
Once I wore that down to cover the IHS, as the base is a little larger than, I flipped it over, and used the sandpaper, which was adhesive-backed to prevent it from sliding. I'd continuously turn it while moving it back and forth, and this not only worked faster for me than a back-forth/turn method, but it also kept the base flat. Keep the fingers as close to the base as possible, lock the arms, and use your torso to move. This will help minimize odd movements, and prevent the heatsink from tipping, which will convex the edge.
If you're really unsure, try contacting a machine shop locally and see what they'd charge; the end result would be very flat.