Atomic Force Microscopy (AFM) was employed to probe the internal structure of living HepG2/C3A cells grown on various commercially-available substrates. In order to understand the driving mechanisms behind the different cell morphologies, the surface properties of these substrates was characterized with AFM and related techniques. The roughness of a 10μm×10μm region of a series of substrates was determined and found to be independent of both coating and culture media, with the exception of thick hydrogel-like coatings. Probing with functionalized tips could not distinguish relative degrees of hydrophobicity under cell culture media, presumably because Debye shielding masks the substrate surfaces. Force spectroscopy was performed on the surfaces to determine exposed surface proteins/polymers intrinsic to the substrate and adsorbed from culture media. Preliminary investigation of cell-mediated substrate reconstruction suggests that the cells secrete large (1000kDa) polymeric molecules at the substrate interface.