The development of biomaterials ensuring proper cell adhesion, polarization, migration and differentiation represents a true enabler for successful tissue-engineering applications. Surface nanostructuring was suggested as a promising method for improving cell-substrate interaction. Here, we study Wharton's Jelly human Mesenchymal Stem Cells (WJ-hMSC) interacting with nanogratings (NGs) having a controlled amount of nanotopographical noise (nTN). Our data demonstrate that unperturbed NGs induce cell polarization, alignment and migration along NG lines. The introduction of nTN dramatically modifies this behavior and leads to a marked loss of cell polarization and directional migration, even at low noise levels. High-resolution focal adhesions (FAs) imaging showed that this behavior is caused by the release of the geometrical vinculum imposed by the NGs to FA shaping and maturation. We argue that highly anisotropic nanopatterned scaffolds can be successfully exploited to drive stem cell migration in regenerative medicine protocols and discuss the impact of scaffold alterations or wear.