"Please note: Boolean operations do not always create nice and clean meshes, so I recommend you do this only as a final step before exporting your object for 3D printing."

Usually this 'final' step creates much more problems then it solves... Things to do afterwards are closing holes, merging points and removing points on an edge. And consider this: Is there an easier way to solve such an operation in another way? Many times there is. You can just as easyly cut out the shapes in the objects that you wish to boolean. This gives alot more control over what happens with the polygons.

Cheers,

Rob