Nemesis is an advanced molecular structure builder. It is able to build a molecule from predefined 3D fragments. Molecules can be visualized in monoscopic and stereoscopic representations. The geometry of the built molecule can be easily measured and manipulated. Nemesis is a modular program, and its functionality can be extended by plugins. For example, it supports imports and exports of chemical formats using the OpenBabel library. This library is also used for geometry optimization.