2D AND 3D Software problem

I see :)

I see it as essentially a sorting problem (I assume the .stl file isn't just a random collection of tuples). Optimising the data handling will be key to speeding things up.

Thanks guys. I think i've found a software that will do it. It seems pretty advanced and a guy i spoke to form the manufacturers says it will do it!

For your info it's called: "OneCNCXR3 Expert Mill software"

Ed

He's the Tec Support guy !

im not sure if this is any use to you but i use hightfields in my work too but in a very different application ,,however your problem seems very simple to me ..if i am correct
you have a map presumably created by point-cloud or splines data or whatever
and you need to mill the bases of your buildings ...meaning that the lowest point in your map would be zero and any increment of hight determined by your method of creation.
if the level of any buildings foundation slab should be determined by the lowest point of contact with the surface or otherwise stepped up or down according to regs or requirements. what you need to do is give a flat hight surface to the regions that are called bases ...the outline vectors would be given a specific hight either as groups or individually and then merged with the ground or surface map
i can see no reason why this cannot be done in autocad, rhino, studio max, cheetah,hexagon,maya,the list goes on. try sketchup its free....but you still have to generate the g code so i recommend looking at artcam after version 7 as they introduced 3d layers its an expensive programme at five grand though
but you could still do this in rhino at a few hundred quid
if your desperate send files to me and ill send you g code back if it works for you id be happy to help..all you need to do is is have the datum for the ground map or lowest point set to zero
and then give each plot or group of plots a hight assuming that you have a scale determined.