See the wiki page on 2D design and layout for context.

Most of the NanoLab tools (and most other microfabrication applications elsewhere!) take as input a GDSII file. These files have a number of layers, and each layer contains some number of polygons. For example, a photolithography tool like mla150 might expose a pattern on a wafer everywhere there is a polygon on either of two particular wafers in a given GDSII file.