Hi,
I use a software (freeware) utility for probing PCB blanks prior to isolation routing to accommodate any bow or warp in the PCB material.
Its called Autloveller.
Mach4 also has a module called mc.Surface which behaves broadly similarly to Autoleveller.
Note the both of the approaches assume a minor deviation from perfectly flat and attempt to 'flatten' the code that runs on that surface,
they are not really designed for forming point clouds for example.
Craig