In order to fabricate high-aspect-ratio microchannels and through holes in a glass substrate for biochip applications, we have been developing a sand blasting technique using PDMS as a mask material, which was patterned using a thick photoresist SU-8 as a mold. The removal rate and surface roughness of a machined glass increased with an increase in applied pressure and a decrease in the distance between a nozzle and a substrate. In this experiment, the removal rate and surface roughness were in the range of 5-300 μm/min and 2-6 μmRz, respectively. Under conditions of relatively low applied pressures ranging 0.2 to 0.3 MPa, uniform cross-sectional profile can be obtained when the nozzle-substrate distance is small. On the other hand, at higher applied pressure of 0.4-0.6 MPa, an increase in the distance was found to be effective.