If you are asking about calibrating the movement of Z (steps per inch) ...
A dial indicator is a std way of measuring movements, easily to 0.001", often 0.0001". It is pretty obvious how you can set it up to measure Z movement, and you can just jog Z a given number of steps then measure the actual displacement.
Do you have a decent vernier?
1) use your approximate calibration on Z to machine a flat surface on a piece of wood, as thick as possible. Call this Z=0.00
2) pocket the wood by a chosen depth according to the approximate calibration. Make the pocket as deep as possible for highest accuracy. Make sure your Z is not going to hit the table before starting the program.
3) measure how deep the pocket really was, and use this to adjust Mach3's calibration factor. If the pocket was deeper than expected, you need to reduce the steps per inch settings.
When carving images (PhotoVCarve?) it is just as important to have the absolute position of the tool properly referenced to the top of the work piece. Are you using a ZeroPlate of some description? IMHO this is a bigger source of error than the calibration, since even an approximate calibration will be within a percent or two. Z=0.00 has to be right to within a few thou.
Cheers!