In-plane orientation of mesochannels in mesostructured silica films is fully controlled by a lithographically formed anisotropic surface morphology of a substrate. The orientation is determined simply by elastic properties of a liquid crystal phase, which appears in the course of the formation of mesostructured silica films through the sol-gel process. When an array of linear microscopic grooves with a round cross section is closely formed on the substrate surface, the cylindrical mesochannels in the films are entirely aligned strictly perpendicular to the grooves, as a consequence of minimization of the total elastic energy. When the surface morphology geometrically fits to the hexagonal arrangement of the mesochannels, the orientation abruptly changes into the direction parallel to the long axis of the grooves. The alignment control based on the elastic property of the liquid crystal phase described in this report does not require any specific chemical interactions between the surfactant molecules and the substrate surface. Therefore, aligned mesostructured silica films with a large structural periodicity can successfully be formed using block copolymer surfactants, which hardly form an aligned mesostructure without the support of external fields. The vapor-phase synthesis, which enables considerable retardation of the solidification process of siliceous species, is the most favorable way, and totally aligned mesostructured silica films with significantly large thickness, more than 1 μm, can be obtained. Appropriate combination of the bottom-up and the top-down nanoprocesses reported in this paper, that is, self-assembly and photolithography, will enable the formation of highly anisotropic nanostructured materials, which will find various practical applications.