An ultra-precision polishing method using magnetorheological (MR) fluids is applied to the powder blasted micro channels fabricated on fused silica glass to improve surface quality and recover optical transmittance. For the experiments, 300 ${mu}m$ micro channels with 600 ${mu}m$ square reservoirs were fabricated on the glass; then, a series of MR polishing were performed. The surface roughness and transmittance of the micro channels rapidly improved after 20 minutes MR polishing. The Measured surface roughness of the final specimen was Ra = 2.2 nm, and transmittance was 99.38% (at wavelength = 1600 nm) of the original specimen. The results of this research confirm that the MR polishing can be a very effective method to improve surface roughness and transmittance by polishing the micro channels on fused silica glass.