when a model is made of multiple objects it just fails to prepare the model correctly, it generates interiors and holes and the "Merge all outlines" tool either fixes the holes but adds random surface planes, or just doesn't change anything.
the first pictures are this http://www.thingiverse.com/thing:441087 model with base settings
the next is with "Merge all outlines" and you can see it plugs the nose hole and adds base floors to the eye sockets for some reason.
te last two is this model http://www.thingiverse.com/thing:758165 and regardless of what is selected, the overlapping internal parts make it go haywire and generate holes.

Cura slices them fine but lacks manual supports and the level of customization so I'd really like to use S3D, but I just cant get it to work with multi part models
any thoughts?