I swear. You kids and your fancy schmancy computerized G-code makers.
Back in my day, we used to have to draw our part out on graph paper and make g-code by hand from that.......up hill both ways through the snow
Have you tried BobCAD? Its not as robust as MasterCAM, but I think it would be better for making waterblocks, as its a 2D program.
You dont really need a 3D enviornments for making waterblocks, it just makes it harder. It takes a little bit to getthe hang of it, but once you do, its pretty fast.