We developed two kinds of the microchip for application to electrophoresis based on both glass and quartz employing the MEMS fabrications. The poly-Si layer deposited onto the bonding interface apart from channel regions can play a role as the optical slit cutting off the stray light in order to concentrate the UV ray, from which it is possible to improve the signal-to-noise (S/N) ratio of the detection on a chip. In the glass chip, the deposited poly-Si layer had an important function of the etch mask and provided the bonding surface properly enabling the anodic bonding. The glass wafer including more impurities than quartz one results in the higher surface roughness of the channel wall, which affects subsequently on the microflow behavior of the sample solutions. In order to solve this problem, we prepared here the mixed etchant consisting HF and NH4F solutions, by which the surface roughness was reduced. Both the shape and the dimension of each channel were observed, and the electroosmotic flow velocities were measured as 0.5 mm/s for quartz and 0.36 mm/s for glass channel by implementing the microchip electrophoresis. Applying the optical slit with poly-Si layer provides that the S/N ratio of the peak is increased as ca. 2 times for quartz chip and ca. 3 times for glass chip. The maximum UV absorbance is also enhanced with ca. 1.6 and 1.7 times, respectively.