You can use sandpaper to smooth it down, just like it was made of wood. The smoother you want it to be, the more effort it will take but it will be worth it. If you try to smooth down the layers as much as possible while you are macheing it will save a lot of time at the end.

Hi there, I have found that when layering paper if you use smaller pieces(fingernail size) on the curved parts of the work it will sit flatter. I know it seems slow work, but works out quicker in the long run. Also you must smooth things down as you go, if it won't sit flat, pull the paper off and put a smaller piece on instead. I work on several items at once, doing only one side at a time to make it easier to handle.