I've got a mesh of a terrain. I'd like to create a simpler version that follows roughly the same shape. I've been using Remove Doubles to do this (which gives me a better result than the Decimate modifier), but have noticed that it can create intersections in the mesh, which causes me problems later on, particularly when using the Boolean modifier.
Original mesh:
When removing doubles (red areas are intersecting faces):
What's the best way to remove these intersections after removing the doubles (or preventing them from happening)? I'm scripting this process, so would love to hear of any solution that doesn't involve manually selecting visible/invisible faces. Thanks!
Edit: Here's the Blend file in case anyone is interested.




Remove Doubles. I'll look into the Shrinkwrap (which I think should be scriptable, viabpy.ops), but haven't had much success with it so far. $\endgroup$