nano-columns were deposited in 2-D and 3-D in the form of well-defined geometries by physical vapor deposition. The films were grown by e-beam evaporation with an angle between source and substrate. The Si nano-columns were deposited in the shape of spiral with two different incoming atomic flux angle so that the manipulation of nano-columns in 3-D (out-of-plane) was obtained. The Si nano-columns were also grown as vertical stick with square, triangle and linear cross sections in 2D (in-plane). Rat bone marrow mesenchymal stem cells (MSCs) were cultured on these different Si nanosurfaces. MTS assay was carried out to determine the cell proliferation and viability based on different nanotopographies. For the evaluation of cell distribution and morphology, a SEM (Scanning Electron Microscopy) analysis was performed. Any CaP deposition on Si nanosurfaces was observed using energy dispersive X-Ray spectroscopy in SEM (SEM-EDX). After 4 days of culture, there was a higher value of cell proliferation on square columns and spiral Si nano-columns grown with 85 of incoming atomic flux. The cell attachment and spreading was also affected by the geometry of Si nano-columns. While there were still cells showing round/spherical morphology with minimal spreading on conventional Si surfaces, most of the cells cultured on different Si nanotopographies attached on the surface and displayed flattened morphology, especially on the square columns surface. Moreover, CaP deposition was discovered on square columns and spiral films with 85 substrate angle. So, it can be concluded that there is a clear correlation between cell responses and nano-sized geometry on Si surface and it is possible to induce cellular differentiation and CaP formation in certain geometrical constraints.