This paper presents a fabrication of polymer microchips with homogeneous material technique due to surface treatment by plasma before sealing. UV laser photoablation was used for fast prototyping of microstructures, and oxygen plasma was used as a surface treatment for both the microfabricated substrate and the polymer cover. It was found that with an oxidative plasma treatment, successful bonding could be achieved without adhesive material between polymer sheets substantially below the glass transition temperature of the polymer. Homogeneous polyethylene terephthalate (PET) microstructures were characterized by scanning electron microscopy (SEM) and analyzed by X-ray photoelectron spectroscopy (XPS) surface analyses after different surface treatments. The electroosmotic flow characteristics including the velocity and the stability over 20 days have been tested and compared to composite channels, in which the cover presents a polyethylene (PE) adhesive layer. Capillary zone electrophoresis in both homogeneous and composite microanalytical devices were then performed and compared in order to evaluate the separation efficiency. In preliminary experiments, a plate height of 0.6 m has been obtained with homogenous microchannels. The surface analysis pointed out that the surface chemistry is of prime importance for the performance of microfluidic separation.