Your problem is too simple - no specific cartography software I know would do only that - generally they do more complex things.
What you need is just a small mathematical program like http://k3dsurf.sourceforge.net/

With that you can plot any 3D surfaces you want. F.ex you can consider that every ressource deposit is a small sphere of varying center and radius and this kind of software will plot all the spheres wherever you want them to be.