Free-standing silica membranes with hierarchical porosity (ca. 300 nm macropores surrounded by 6-8 nm mesopores) and controllable mesopore architecture were prepared by a dual-templating method, with the structural design aided by mesoscale simulation. To create a two-dimensional, hexagonal macropore array, polymeric colloidal hemisphere arrays were synthesized by a two-step annealing process starting with non-close-packed polystyrene sphere arrays on silicon coated with a sacrificial alumina layer. A silica precursor containing a poly(ethylene) oxide-poly(propylene oxide)-poly(ethylene) oxide (PEO-PPO-PEO) triblock-copolymer surfactant as template for mesopore creation was spin-coated onto the support and aged and then converted into the free-standing membranes by dissolving both templates and the alumina layer. To test the hypothesis that the mesopore architecture may be influenced by confinement of the surfactant-containing precursor solution in the colloidal array and by its interactions with the polymeric colloids, the system was studied theoretically by dissipative particle dynamics (DPD) simulations and experimentally by examining the pore structures of silica membranes via electron microscopy. The DPD simulations demonstrated that, while only tilted columnar structure can be formed through tuning the interaction with the substrate, perfect alignment of 2D hexagonal micelles perpendicular to the plane of the membrane is achievable by confinement between parallel walls that interact preferentially with the hydrophilic components (PEO blocks, silicate, and solvent). The simulations predicted that this alignment could be maintained across a span of up to 10 columns of micelles, the same length scale defined by the colloidal array. In the actual membranes, we manipulated the mesopore alignment by tuning the solvent polarity relative to the polar surface characteristics of the colloidal hemispheres. With methanol as a solvent, columnar mesopores parallel to the substrate were observed; with a methanol-water mixed solvent, individual spherical mesopores were present; and with water as the only solvent, twisted columnar structures were seen.