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Surface micropatterns are relevant instruments for the in vitro analysis of cell cultures in non-conventional planar conditions. In this work, two semiconductors (Si and TiO2) have been micropatterned by combined ion-beam/chemical-etching processes leading to selective areas bearing nanorough features. A preferential affinity of human mesenchymal stem cells (hMSCs) for planar areas versus nanotopographic ones is observed. Fluorescence microscopy after β-catenin staining suggests that hMSCs adhesion is inhibited on nanostructured porous silicon areas. This has a direct impact in the development of actin fibers and suggests different cell migration mechanisms on the materials of a micropattern. hMSCs organization on nanotopographic micropatterns has been modeled by using a simplified random walk approach. The model attributes preferential cell mobilities on the nanotopographic areas with respect to the planar and considers purely stochastic movement with no inertial term. Simulations of the cell distribution have been run on 1D and 2D micropatterns and compared with the real hMSC cultures. The simulations allow defining two regimes for cell organization as a function of cell density. hMSCs ordering on planar areas is diffusion-induced in most micropatterns but constriction forced disorder appears for high cell densities. The relative mobility on the planar versus nanotopographic areas can be used as a quality indicator of the nanotopography contrasts in the diffusion induced ordering regime. It is shown that the relative mobility is favorable for the TiO2 versus the Si based system, and allows envisaging its use for the calibrated design of nanotopography based micropatterned materials.