Tendon is commonly injured, heals slowly and poorly, and often suffers re-injury after healing. This is due to failure of tenocytes to effectively remodel tendon after injury to recapitulate normal architecture, resulting in poor mechanical properties. One strategy for improving the outcome is to use nanofiber scaffolds and mesenchymal stem cells (MSCs) to regenerate tendon. Various scaffold parameters are known to influence tenogenesis. We designed suspended and aligned nanofiber scaffolds with the hypothesis that this would promote tenogenesis when seeded with MSCs. Our aligned nanofibers were manufactured using the previously reported non-electrospinning Spinneret-based Tunable Engineered Parameters (STEP) technique. We compared parallel versus perpendicular nanofiber scaffolds with traditional flat monolayers and used cellular morphology, tendon marker gene expression, and collagen and glycosaminoglycan deposition as determinants for tendon differentiation. We report that compared with traditional control monolayers, MSCs grown on nanofibers were morphologically elongated with higher gene expression of tendon marker scleraxis and collagen type I, along with increased production of extracellular matrix components collagen (p = 0.0293) and glycosaminoglycan (p = 0.0038). Further study of MSCs in different topographical environments is needed to elucidate the complex molecular mechanisms involved in stem cell differentiation.