The widespread interest in micro total analysis systems has resulted in efforts to develop devices in cheaper polymer materials such as polydimethylsiloxane (PDMS) as an alternative to expensive glass and silicon devices. We describe the oxidation of the PDMS surface to form ionizable groups using a discharge from a Tesla coil and subsequent chemical modification to augment electroosmotic flow (EOF) within the microfluidic devices. The flow performance of oxidized, amine-modified and unmodified PDMS materials has been determined and directly compared to conventional glass devices. Exact PDMS replicas of glass substrates were prepared using a novel two step micromolding protocol. Chemical force microscopy has been utilized to monitor and measure the efficacy of surface modification yielding information about the acid/base properties of the modified and unmodified surfaces. Results with different substrate materials correlates well with expected flow modifications as a result of surface modification. Oxidized PDMS devices were found to support faster EOF (twice that of native PDMS) similar to glass while those derivatized with 3-aminopropyl triethoxysilane (APTES) showed slower flow rates compared to native PDMS substrates as a result of masking surface charge. Results demonstrate that the surface of PDMS microdevices can be manipulated to control EOF characteristics using a facile surface derivatization. methodology allowing surfaces to be tailored for specific microfluidic applications and characterized with chemical force microscopy.