Benjamin, a few things here. Go to your drawing parameters (right click in bottom right gray area of your SWE window) and uncheck "show wipeout frames" to hide the green frames.
Also, SWE will assume a rectangular wipeout if your symbol DOES NOT have a wipeout specified by you! So if your footprint is non-rectangular, I recommend going into the symbol and adding a wipeout yourself following the outer boundaries of that symbol.
Try the Erase background button and see if that handles it ont he fly? but I recommend adding to the symbol so it's cleaned up for good.
Additionally you can set the "order" of the symbols in relation to their background, your symbols set to front should obliterate the background if a proper wipeout has been added to the symbols. If something else is going on and those backgrounds are not whiting out with the symbol on top, contact your VAR, that will need a little more attention.
I didn't know anything about wipeout frames. Now I will go add them to all my parts.