Microfluidic structures in poly(dimethylsiloxane) (PDMS) are usually fabricated by optically patterning a resist and subsequently transferring this pattern to PDMS. Such microsystems suffer from reduced resolution, which in turn inhibit the manipulation of sub-micron scale entities such as bacteria, as well as their optical properties (e.g. long period gratings and radiation losses). In this paper we discuss how electron beam lithography (EBL) can be employed in prototyping SU8 moulds and nanostructures for poly(dimethylsiloxane) (PDMS) based microfluidics and optofluidics. In comparison to conventional optical methods, direct patterning of SU8 with an electron beam enabled both sub-and few micron scale structures with reduced complexity and duration. We will also discuss how to synthesize optofluidic circuits with this method and discuss our preliminary results on how such sub-micron scale structures can be employed in the optofluidic analysis of bacteria.