Thanks for your reply, first of all. I might be able to upload an STL file as an example, have to organize one first. Besides that, I was hoping for a software tip, that minimizes manual 3D edits, since a) I never worked with 3D software and b) the more manual is involved, the less usable is the method for hundreds of objects.

In my simple view on this, I was hoping for a software function, that just traces the border of the terrain mesh, extrudes it down for a given amount of meters (= walls), and closes the base (= bottom), which would result in the water proof block 3D printers require. Anyone knowing anything like this?

STL seems the format of choice in the 3D printer world, along with VRML, that's why I use it...