The surface morphology of liquid crystal alignment layer has been investigated by using Brewster angle microscope(BAM) for the first time. The samples used in this work for liquid crystal alignment layer were mechanically rubbed polyimide films. The rubbing pattern on this layer has been analyzed with the terms of microgroove and rubbing induced optical birefringence. For the mechanically rubbed surface, the geometrical factors of microgroove play the major role for the formation of rubbing pattern. We propose that the BAM can be used as a powerful tool not only for observing the rubbing pattern, but also for inspecting the surface defects.