Remove intersections between many objects I have a bunch of objects in my scene that are intersecting each other. Is there any way, without creating a million boolean modifiers on each, to remove all mesh intersections in my scene? 



Maybe there's a script to apply a bunch of booleans to every object?
You may use a Direct Union of a BoolTool add on.


Activate the add on in User Preferences (Ctrl+Alt+U).


Select all the spheres with Shift+RMB, then press Spacebar and type direct union.


If you want to separate each object use Linked Flat Faces option.


Select one face of the sphere, go to Select-->Linked Flat Faces (or use a Shift+Ctrl+Alt+F shortcut). Increase the Sharpness value in a Tool Shelf. Then press P-->Selection to separete the selection.