This article reveals the enabling aspects of nanografting (an atomic force microscopy-based lithography technique) in surface physical chemistry. First, we characterize self-assembled monolayers and multilayers using nanografting to place unknown molecules into a matrix with known structure or vice versa. The availability of an internal standard in situ allows the unknown structures to be imaged and quantified. The same approaches are applied to reveal the orientation and packing of biomolecules (ligands, DNA, and proteins) upon immobilization on surfaces. Second, nanografting enables systematic investigations of size-dependent mechanics at the nanometer scale by producing a series of designed nanostructures and measuring their Young's modulus in situ. Third, one can investigate systematically the influence of ligand local structure on biorecognition and protein immobilization by precisely engineering ligand nanostructures. Finally, we also demonstrate the regulation of the surface reaction mechanism, kinetics, and products via nanografting.