We have used an embossed plastic microfluidic system for rapid electrophoretic separation of small molecules and electrospray ionization. We have also visualized the separation of compounds by observation of dyes in microfluidic systems and electrospray from the edge of the device. We used a lithographically produced silicon master to emboss channels in ZEONOR 1020R plastic. An oxygen plasma or chromic acid was used to convert the plastic channel surface from hydrophobic to hydrophilic for the separation of molecules in aqueous solution. The channel was scaled by thermal bonding of a cover piece of the same plastic material. The microfluidic device for electrophoretic separation and fluorescence detection had a separation channel 50 μm wide, 20 μm deep and 3.0 cm long. This was used to separate two dye molecules, Rhodamine B and Texas Red. The microfluidic device for electrospray ionization directly from the chip had a separation channel 30 μm wide, 10 μm deep, and 10 μm wide, terminating in a nozzle-like pyramid fabricated at the edge of device. The sample volume injected through the cross junction for fluorescence detection device was approximately 1.2 nl and two dyes were separated within 8 seconds with the application of an electric field 300 V/cm.