Topographical factors of scaffolds play an important role in regulating cell functions. Although the effects of alignment topography and 3D configuration of nanofibers as well as surface stiffness on cell behavior have been investigated, there are relatively few reports that attempt to understand the relationship between synergistic effects of these parameters and cell responses. Herein, the influence of biophysical and biomechanical cues of electrospun polyurethane scaffolds on mesenchymal stem cells (MSCs) activities was evaluated. To this aim, multiscale bundles were developed by rolling up the aligned electrospun mats mimicking the fascicles of tendons/ligaments and other similar tissues. Compared to mats, the 3D bundles not only maintained the desirable topographical features (i.e., fiber diameter, fiber orientation, and pore size), but also boosted tensile strength (∼40 MPa), tensile strain (∼260%), and surface stiffness (∼1.75 MPa). Alignment topography of nanofibers noticeably dictated cell elongation and a uniaxial orientation, resulting in tenogenic commitment of MSCs. MSCs seeded on the bundles expressed higher levels of tenogenic markers compared to mats. Moreover, the biomimetic bundle scaffolds improved synthesis of extracellular matrix components compared to mats. These results suggest that biophysical and biomechanical cues modulate cell‐scaffold interactions, providing new insights into hierarchical scaffold design for further studies.This article is protected by copyright. All rights reserved