Here’s a little example I’ve cooked up of three little blocks placed into a large block.
As you can see, freestyle lines are being drawn for the hidden parts of the little blocks. This is bad.
Without merging the geometry of the little blocks with the big block, how can I fix this?
Blender 2.78
Windows
Blender Render
default scene and lighting, just duplicated cubes, resized and elongated them, placed them into the big cube, and toggled on Freestyle