Yes, sort of...
You can't really 'cut' away any parts, but you can give various triangles a tag to tell the game to not draw them. After you have your LOD positioned, press "shift+F", that will bring up a box called "Edit Facet Flags".
Now, depending on the orientation of you LOD and, I'm assuming, other brushes, you can highlite 'facets' or triangles to 'tag'. What I've done mostly is just used the 'Delete' option. Example: you draw a trench line and the parapets stick up a couple units above the LOD. Now, the LOD in-game is covering the trench...assuming right angle design... Just use the shift-F function, then: press 'Ctrl+Shift+LEFT MOUSE BUTTON' over the triangles that you want to 'delete' or that you want to use any other option on. They will turn white/highlited in the 3d view.
After you have the sections selected/highlited, simply click in the toggle box next to the function flag you want to give that selection. Compile and run around that area. They should be gone....you CAN FALL through these areas if there isn't another brush below them!
Also, be very careful when using this function AFTER dragging around the terrain points. As you manipulate the terrain, it gets harder to tell if you have a triangle highlited or not. Best to do this BEFORE you change any terrain points, i.e. the LOD is FLAT...but, can't always know where you're going but when you can, do it flat.
There are definitions and some examples in the files that came with the MOHAA documents, forget which one, but I think it was about LOD specifically and will define all those facet flag options, good reading, at least 8 or 9 times till you grasp and remember it all!
