Molecular alignment of liquid-crystal affects on electro-optical characteristics in display device. Rubbing on the alignment surface is most reliable process for obtaining uniform molecular alignment in manufacturing. In this paper, fine structures of the surface of the alignment substrates were observed by atomic force microscope (AFM) and the mechanism of liquid-crystal molecular alignment was investigated. As the results, the rubbing process induces geometrical anisotropy on the substrate in specific condition and has not monotonous dependence of the rubbing condition.