The electro-nanopatterning and mechanism of pattern formation in azobenzene-containing layer-by-layer (LbL) ultrathin films is described using surface probe microscopy techniques. First, arrays of nanodots were patterned on these films to investigate applied time at constant voltage bias dependence in electro-nanopatterning. The anisotropic mass transport and polar alignment of the azobenzene-containing films were observed after applying the electric field and heating the sample locally with the cantilever tip. On the basis of this novel phenomenon, small-sized surface relief gratings (SRG)s and their alignment were fabricated and observed by current-sensing atomic force microscopy. The rate of mass transport for the polymer is mainly controlled by the applied time at constant voltage bias between the cantilever and the electrode/substrate.