We report a simple and facile technique for creating complex mesoscale patterns with two-dimensional (2-D) orders on the surface of a sol gel derived silica thin films using a combination of a topographically patterned stamp and a substrate, each having a one-dimensional (1-D) grating structure (stripes). The self-organized pattern formation results as a consequence of capillary flow of the sol film in liquid state under a confining stamp. The key novel aspect of the work lies in using a topographically patterned substrate, dip coating on which results in a film with an undulating top surface. When a grating stamp is brought in conformal contact with such a film in a manner so that the direction of the stamp stripes are at right angles to the direction of the undulations on the film surface, a periodically ordered spatial variation in the extent of contact between the film and the stamp results. Subsequent capillary flow of the liquid sol along the stamp walls occurs only at the locations where the stamp surface and the film are in direct contact, resulting in an array of pillars with 2-D order. We further show that the morphology of the final patterns can be tailored by varying various parameters such as the initial film thickness, wettability of the stamp, and periodicity of the substrate. We further discuss the gradual oxidation of the sol film with progressive thermal annealing and the associated shrinkage of the structures in terms of pattern dimensions. Generation of meso patterns with 2-D order on an inorganic sol gel film surface using a stamp and a substrate, each having strictly 1-D features, is the key novel aspect of the work, as it is a rare example when patterns other than a mere negative replica of a stamp are created on a sol gel thin film by any soft lithography technique.