A novel approach for the synthesis of advanced functional inorganic materials with atomic-scale control over the size of periodic features on the sub-30 nm scale is presented. The key innovative aspect of this technique is the direct, bottom-up formation of a two-dimensional periodic array of spatially separated nanostructures in a self-organized thin-film porous template. This thin-film template is fabricated via biologically inspired hierarchical self-assembly of organic surfactant molecules in the presence of inorganic charged silicate species. The removal of organic molecules from such an organic/inorganic hybrid system creates a periodic array of pore channels of ∼3-30 nm diameter inside the thin-film silica template. This porous template is employed as a shadow mask to directly grow various functional nanostructures inside the confined environment of the periodic pore arrays. In the present study, silicon nanostructures were grown inside the templates by both chemical and physical (sputtering) vapor deposition. The quantum size effect was clearly pronounced in the room temperature photoluminescence spectra of the samples prepared by sputtering from a Si target, which makes the approach highly promising for the fabrication of nanoscale optoelectronic devices.