When I print a space filling model from Chem3D or another application, some models are missing or have a thick border around some atoms.
Space filling models are created in Chem3D by a technique called regions. Some applications and printer drivers cannot handle regions. The solution is to use the Copy as Bitmap option in the Chem3D 5.0 Edit menu or Save As Bitmap option. This will produce a bitmapped image of the model, which you should be able to print properly.