3D layers are a way for you to import true 3D models into Moho. When a 3D layer is rotated in space (or the camera moves around it), you actually see that backside of the model. Moho supports importing OBJ files into 3D layers - OBJ is a common 3D file format that most 3D programs can read and write.
When importing OBJ files, Moho will also load any associated material file, importing the objects' colors and texture maps.
3D layers can also be used with skeletons. Using a bone layer, you can warp a 3D model by moving bones around. Keep in mind that while 3D layers are truly three-dimensional, bone layers are only 2D. So, any manipulation you do with bones is going to be limited to some degree.
Because Moho is not a true 3D program, not all 3D features are supported. In particular, lighting. Any 3D model you import will be flat shaded. However, because Moho does support texture maps, you can simulate lighting if a texture map has lighting effects "baked" into it.
Here are some 3D programs we recommend for use with Moho. There are tons more out there. We recommend these because they're good quality, and are either free or inexpensive. If you want to use a high-end, expensive 3D program, you probably already know what you're looking for.
P.S. When preparing a 3D model for use with Moho, it's usually a good idea to triangulate the model before exporting it as an OBJ file. This will eliminate any problems with concave or complex faces.