A simple procedure to convert protein data bank files (.pdb) into a stereolithography file (.stl) using VMD software (Virtual Molecular Dynamic) is reported. This tutorial allows generating, with a very simple protocol, three-dimensional customized structures that can be printed by a low-cost 3D-printer, and used for teaching chemical education topics. With the use of the free licensed and multiplatform software, colored input geometries can be obtained by a simple-click modification procedure in order to generate .obj and .mtl files. An easy protocol to create personal .pdb files for 3D-printing technology is also reported.