Atomic Force Microscopy (AFM) has been widely used in surface characterization due to its unprecedented high spatial resolution. Taking advantage of the very strong and localized tip-sample interactions, AFM can also be utilized as a powerful tool to perform the surface nanolithography. Here we will present an AFM-based fabrication method known as nanografting and its use to produce nanostructures with precisely controlled size, geometry, functionality and local environments including under electrochemistry control at the nanometer-scale within a self-assembled monolayer (SAM) surface. Examples of application of nanografting such as positioning of biomolecules on surface, regulation of the lateral heterogeneity of mixed SAMs, and the size-dependent study of physical properties of materials with nanometer scale precision will be presented to demonstrate that AFM lithography provides us a necessary platform for studies in nanotechnology and material science.