There is a nice paper on 3D printing molecular structures "How to print a crystal in 3D"
However, the method is a bit difficult, it requires many steps and strange soft like Blender. The most important problem is that Blender exports shell-like (mesh) files, rather than convenient solid objects. Converting meth into a solid looks like a simple task, but my FreeCad was unable to do it - it is far too complex task. I needed it to manually make supporting material.
Here I have devised a very simple method to obtain SOLID 3D model of a structure. You need only 2 tools: FreeCad and Excel + XYZ file of your structure.