Poly(dimethylsiloxane) (PDMS) has become a ubiquitous material for microcontact printing, yet there are few methods available to pattern a completed PDMS stamp in a single step. It is shown here that electron beam lithography (EBL) is effective in writing patterns directly onto cured PDMS stamps, thus overcoming the need for multiple patterning steps. Not only does this method allow the modification of an existing lithographic pattern, but new 3D features such as cones, pits, and channels can also be fabricated. EBL can also be used to fabricate PDMS masks for photolithography whereby 1: 1 pattern transfer into a photoresist is achieved. Additionally, direct EBL writing of surface chemical features has been achieved using a PDMS stamp coated with a self-assembled monolayer. An electrostatic mechanism appears to be operative in the EBL patterning process, as supported by calculations, thermogravimetric analysis, time-of-flight secondary ion mass spectroscopy, optical and atomic force microscopy, and chemical functionalization assays.