Clean Internal Geometry

I am going bonkers trying to clean my models' internal geometry for printing. One of the big problems is when I put a shirt or pants on a model, for example, the layer of 'skin' beneath the 'cloth' gives the appearance of a very thin wall (although the two meshes are connected). I have spent hours trying to clean one to no avail. I have ignored this problem in the past and had successful prints, but I have also had several rejections because of these internal vertices. It seems to me there should be either a script or program which can either detect the internal vertices and delete them, or create a new external manifold mesh around the faces of the object and delete the interior. Have been searching for hours with no luck. Any suggestions?

As long as each individual shell is a 'watertight' mesh with the normals all facing one way, Shapeways upload processing will take care of the joins (if they overlap) and basically ignore internal geometry. The problems you describe imply that the shells are not correctly defined. When I say shell here, in your models one shell might be the body, another shell might be an item of clothing.

Netfab Basic can help you find the problems with your meshes.

It would probably help if you would write which program and/or file format you are using. For STL files, the netfabb cloud service usually
does a good job of fusing shells (though you must beware of rounding errors or different tolerance values used by different programs - what
might look "connected" in one program might be "very closely adjacent" in another).
Also check orientation of the face normals of your models - if patches appear to be "inside out" due to their coordinates being listed in the wrong
sequence, computer programs have a hard time figuring out which is the correct solution, or if there is a closed 3d object at all. (Internal geometry
as such should not be a problem, as long is it completely enclosed in some outer shell it should be deleted automatically by shapeways' software.
So the actual problem could also be that the perceived "surface" of your model has an unintended hole somewhere)

I see from this thread you use Blender and Netfab already.

And that we have already been discussing these exact same topics ...

Yes, I had mentioned this in another thread but that was kind of a different question so I started this one with a specific focus on seeing if anyone knows of software that can clean out the internal geometry automatically. Even with Netfabb, cloud.netfabb, and blender I'm still getting models that read as thin walls because of stray faces inside (ie. they look pretty solid if you cut them open in Netfabb and pass the cloud checks, but if you click on them with the measuring tool they read as having a thin wall because of a stray section of faces below the surface). Perhaps this doesn't really affect the printing process anyway, but I think a good program that could do this would certainly help a lot of people trying to make manifold meshes both for 3D printing and paper-folding.

I also have some poorly built older models I made that are so messy I pretty much need to redo them. I am hoping to save them.

Now Meshlab has a feature which allows it to create a mesh around a point cloud from a 3D scanner, but doesn't seem to work for me on a regular mesh. What I think would be great is a program that would just wrap a new topography around the mesh object and delete the interior. DO any of the commercial programs do this?

I have had mixed luck with it, but that's essentially what the Alpha Shape modifier in Meshlab does.

I kind of understand what you are trying to do, but not why you want to do it. The point is that if you make each shell correctly you never have to worry about the internal geometry.

I would investigate more why your shells are not working and try to rectify that. If the Solidify Modifier does not give you what you want try simply extruding and tidying up any glitches.