Although silica nanoparticles are used as building blocks in nature and synthetic mesostructures, the influence of nanoparticle characteristics on the assembly and disassembly of mesostructured silica has not been investigated. We demonstrate that nanoparticle size and size distribution allow us to control the assembly of silica-type mesostructures and that, because of the discrete nature of nanoparticles, we can disassemble these mesostructures into a rich variety of structural building units. When assembling mesostructures, nanoparticles undergo size-dependent segregation once the nanoparticle diameter exceeds a critical size threshold, which is approximated by the root-mean-square end-to-end distance of the hydrophilic block of the block copolymer. Using this phenomenon, we direct gold-silica core-shell nanoparticles into the segregated regions of silica-type mesostructures, demonstrating the ability to precisely place nanoparticles and create compositionally heterogeneous, functional mesostructures. We further show that, because the mesostructures are composed of nanoparticles, they can be disassembled into nanotubes, hexapods and other complex, well-defined structural units, thereby introducing the concept of retrosynthesis to materials chemistry. Our results demonstrate how nanoparticle characteristics influence the structure and properties of nanoparticle-derived mesostructures. Size-dependent segregation and disassembly should improve structure control at the near-molecular level and should be applicable to a wide range of nanoparticle-derived mesostructures.