When we were looking at confocal scopes, we were very impressed withthe
Mol Dynamics software for dealing with this very problem. Their program
is called Image Space I think, and is now available for non MolDyn
setups, runs on Unix boxes. It *was* extremely nice and interactive; it
probably still is. They (AKA David Hanzel) took great pains to point out
the ease of obtaining an "orthogonally correct" three-dimensional image
with their software. I'm sure, however, that Vital Images wouldn't allow
such an important feature to be unavailable. Just, maybe, not
immediately apparent.