Buckminsterfullerene, a molecule made of 60 carbon atoms, and having the shape of a truncated icosahedron, is easily modeled with Stella 4d: Polyhedron Navigator (see http://www.software3d.com/Stella.php to try or buy this program). The first image shows the”ball and stick” version used by chemists who want the bonds between atoms to be visible.
The second model is intermediate between the ball-and-stick version, and the space-filling version, which follows it.
Here’s the “closely packed” space-filling version, taken to an extreme.
Which version better reflects reality depends on the certainty level you want for molecular orbitals. A sphere representing 99% certainty would be larger than one for 95% certainty.