Biomaterials can control cell and nuclear morphology. Since the shape of the nucleus influences chromatin architecture, gene expression, and cell identity, surface topography can control cell phenotype. This study explores how surface topography influences nuclear morphology, histone modifications, and expression of histone-associated proteins through advanced histone mass spectrometry and microarray analysis. We found that nuclear confinement is associated with loss of both histone acetylation and nucleoli abundance, while pathway analysis revealed a substantial reduction in gene expression associated with chromosome organization. In light of previous observations where we found a decrease in proliferation and metabolism induced by micro-topographies, we connect these findings with a quiescent phenotype in mesenchymal stem cells, as further shown by a reduction of ribosomal proteins and the maintenance of multipotency on micro-topographies after long-term culture conditions. Furthermore, this influence of micro-topographies on nuclear morphology and proliferation was reversible, as shown by a full return of proliferation when re-cultured on a flat surface. Our findings provide novel insights on how biophysical signaling influences nuclear organization and subsequent cellular phenotype.