The extracellular matrix (ECM) exhibits tissue-specific topography and composition and plays a crucial role in initiating the biochemical and biomechanical signaling required for organizing cells into distinct tissues during development. How single cells assemble into structures featuring specific shapes in response to external cues is poorly understood. We examined the effect of substrate nanotopography on the morphogenesis of several types of epithelial cells and found that in response to the topography, Calu-3 and MDCK-II cells formed organoids that closely resemble their morphology in vivo. This finding represents the first demonstration that substrate nanotopography, one of the first physical cues detected by cells, can by itself induce epithelial tissue-like organization. Our results provide insights, in terms of a new aspect of ECM topography, into the design of future tissue-engineering systems and the study of mechanosignaling in the epithelium during normal development and tumor progression.