Bioinspired bottom-up assembly and layer-by-layer (LbL) construction of inorganic materials from lithographically defined organic templates enables the fabrication of nanostructured systems under mild temperature and pH conditions. Such processes open the door to low-impact manufacturing and facile recycling of hybrid materials for energy, biology, and information technologies. Here, templated LbL assembly of silica was achieved using a combination of electron beam lithography, chemical lift-off, and aqueous solution chemistry. Nanopatterns of lines, honeycomb-lattices, and dot arrays were defined in polymer resist using electron beam lithography. Following development, exposed areas of silicon were functionalized with a vapor deposited amine-silane monolayer. Silicic acid solutions of varying pH and salt content were reacted with the patterned organic amine-functional templates. Vapor treatment and solution reaction could be repeated, allowing LbL deposition. Conditions for the silicic acid deposition had a strong effect on thickness of each layer, and the morphology of the amorphous silica formed. "Defects" in the arrays of silica nanostructures were minor and do not affect the overall organization of the layers. The bioinspired method described here facilitates the bottom-up assembly of inorganic nanostructures defined in three dimensions and provides a path, via LbL processing, for the construction of layered hybrid materials under mild conditions.