S3D is a very fine slicer, but it has some quirks and annoyances, and this one is particularly irritating. Instead of many words, here's a picture:
This is just a simple plate where there are some pegs protruding upwards. The issue is that S3D insists on breaking up the top layer with holes where these pegs are, instead of just creating a solid foundation with unbroken top layers on which the pegs are printed. The way S3D does this makes the peg weaker, and the top layer finish less nice, since it doesn't lay down continuous layers.
In addition to this, it also takes slightly more time to print, since this behavior makes for more travel moves. It just isn't a good way of doing it, and even though I use S3D for everything, I tested this same STL in one of the free slicers, and that one did this the proper way with solid top layers and then the pegs.
Is there some way to fix this in S3D that I haven't thought of?