> Is there anyway to subsequently step through the 3D structure and
> examine it, as it were, from the inside?
Image > Stacks > Orthogonal Views does something like this, but perhaps
you are looking for a 3D clipping plane, which I think the 3D Viewer
currently lacks. You could try adjusting the threshold and transparency
(3D Viewer, Edit > Attributes). You could also try Drishti, a freeware
3D renderer:
http://anusf.anu.edu.au/Vizlab/drishti/index.shtmlMichael