The Nanometer Pattern Generation System (NPGS) provides a user-friendly environment for the delineation of complex structures using a commercial electron microscope. NPGS is designed to be extremely flexible, yet easy to use. There are three basic steps to the pattern generation process: pattern design, parameter run file creation, and pattern writing with alignment for multilevel lithography. Patterns are created using DesignCAD, which is a commercial computer-aided-design program. Once a pattern is designed, the exposure conditions for the different drawing elements in the pattern are entered into a "Run File". NPGS can be used in a turnkey fashion with minimal user interaction, or the user can have complete control over the pattern writing - even writing patterns that were not called for in the original run file.