A liquid crystalline block copolymer, composed of poly(ethylene oxide) (PEO) and polymethacrylate (PMA)-bearing azobenzene (Az) mesogen side chains, uniquely forms perpendicularly oriented PEO cylinders in a film on various substrates, independent of the substrate surface energy. In this paper, it is revealed that the perpendicular cylinders are formed at the air interface of the block copolymer film, as the perpendicular cylinders and liquid crystal structures were observed only in the vicinity of the air interface for a block copolymer film annealed for a short period of 5 s. On the basis of this mechanism of air-interface-induced perpendicular cylinder formation, we developed a surface covering method to prevent the perpendicular cylinder formation and instead induce parallel cylinder formation. Moreover, uniaxial cylinder films were fabricated by a combination of the surface covering and substrate rubbing methods. The surface covering layer for controlling cylinder orientation can be removed to utilize the block copolymer film for templating.