We report a simple approach to the formation of 3D colloidal nanoparticle structures incorporating enclosed mesoscopic structures through a simple process of spin-coating-driven directed self-assembly onto lithographically defined polymer templates. Removal of the buried polymer patterns by high temperature calcination results in the formation of hierarchically enclosed channels, continuous networks, isolated cavities, and multilayered structures with high stability and environmental resistance. These channels are used to investigate the transport of DNA molecules in constrained geometries.