In smectic liquid crystals, the arrangement of molecules into layers frequently leads to the spontaneous formation of focal conic domains (FCDs), in which the layers organize around focal curves in the form of conic sections. Thin-film smectics permit robust self-assembly of FCD lattices, which have been studied for device applications. We investigate the influence of nontrivial confining boundary conditions specifically, a topographically patterned substrate on the arrangement and structure of FCDs. Topographic confinement is shown to produce controllable FCD lattices, with the patterning at the substrate propagating into the bulk. When topographic confinement is weakened, a variety of new hierarchical FCD arrangements are observed. We study these disparate behaviors in a single theoretical picture, and discuss approaches to new theoretical challenges presented by the complicated smectic structures that join together neighboring FCDs.