Mesenchymal stem cells (MSCs) as adherent stem cells are being increasingly used as a therapeutic cell source, thus developing a better understanding of how to control MSC fate choice is an increasingly important task. Unlike the well known chemical cues, the biophysical properties of the surrounding extracellular environment, such as the appropriate spatial display of adhesion sites and environment stiffness should be clarified. The atomic force microscopy (AFM)-based technique called force spectroscopy mapping (FSM) was applied for examination biophysical properties such as elasticity and adhesion site size and spacing. Using the indentation, the spatial changes in the mechanics of poly(vinyl pyrrolidone) (PVP) and poly(acrylamide) (PAam) hydrogels were detected. PVP hydrogels had very heterogeneous elastic moduli as a function of hydrogel position as well as the amount of crosslinker. PAam hydrogels were a much more homogeneous substrate, showing little spatial variation in moduli. Coupled with chemical-functionalized probe, the technique of chemical FSM (CFSM) was shown the capability of recognizing sub-micron adhesive sites from probe retraction studies. By functionalizing the probe to recognize the charged surface of copolymers, the spatial display of adhesion sites in diblock copolymer foams was investiaged. Prepared by high internal phase emulsion templating using amphiphilic copolymers of polystyrene- block-polyacrylic acid and polystyrene-block-polyethylene oxide, the porous foams have been synthesized and characterized. With nanoscopic domains of cell inert and active chemistries mimicking native matrix, the nanodomains of adhesive sites were detected by CFSM. Protein adsorption on surfaces was examined in spatially macro-, micro-, and nanoscopic level. MSCs from different cell sources of human-embryonic stem-mesoderm progenitors (hES-MPs) and human bone marrow derived-mesenchymal stem cells (hBMSCs) were examined by quantitative PCR to assess their expression of myogenic, adipogenic, and osteogenic genotypes as a result of their interaction with the foams of varying composition. Interestingly, without the induction media, hBMSCs expressed adipogenic genes and proteins on 'patchy' matrices where adhesive nano-domains were present. More interestingly, and their expression depends on stem cell origin: marrow-derived and mesenchymal progenitor cells exhibit fundamentally different differentiation patterns, adipo- and osteogenic, respectively. Together these data for the first time implicate adhesion as a complex regulator of cell fate