The Nanorex website describes the software:
NanoEngineer-1™ is a 3-D molecular engineering program. It includes both a sophisticated CAD module for the design and modeling of atomically precise components and assemblies, and a molecular dynamics module for simulating the movement and operation of mechanical nanodevices. NanoEngineer-1 is currently under development and is scheduled for release in spring 2007.
Image source: Copyright 2006, Nanorex
Within the site's download area, you can find specifications for the various machines shown in the gallery, including length, width, and number of atoms.