Nanobiomaterials are introducing new capabilities to coordinate cell selection, growth, morphology, and differentiation. Herein, we report that tuning the geometry of ordered arrays of nanopillars (NP) elicits specialized morphologies in adherent cells. Systematic analysis of the effects of the NP radius, height, and spacing reveals that stem cells assume either flattened, polarized, or stellate morphologies in direct response to interpillar spacing. Notably, on NPs of pitch near a critical spacing (d(crit) ≈ 2 μm for C3H10T1/2 cells), cells exhibit rounding of the cell body, pronounced polarization, and extension of narrow axon-like cell projections aligned with the square lattice of the NP array and extending hundreds of micrometers. Furthermore, increasing the NPs' aspect ratio from 12:1 to 50:1 to produce NPs with a corresponding reduction in the NP bending stiffness of 2 orders of magnitude amplified the cellular response and resulted in a previously unseen degree of cell polarization and alignment. The rapid morphological transformation is reproducible on surfaces that maintain key parameters of the NP geometry and spacing, is influenced by the cell seeding density, and persists for different stem cell lines and primary mesenchymal stem cells. The demonstrated ability to support various morphogenetic trends in stem cells by simply tuning the geometry of the NP substrates provides a stepping-stone for the future design of scaffolds where cellular morphology and alignment are crucial.