Yes. In Pep Designer 3 (not Viewer), right click on the 2d view and choose color edge (or press ctrl+e). Pick your color, the types of lines you want colored (cut lines, valleys, mountains, & hidden), and whether you want to paint/pick color/erase those line types. After that, click and drag over the area/lines that you want colored. To easily distinguish mountains from valleys, I like to color my valley folds green, and my mountain folds black. But that's just me. You can pick whatever colors you want to use.
Not sure if these instructions work in Pep Designer 2 since I don't have it, but they should at least be similar.
