AFM based lithography method is a powerful method for not only to create nanoscale structures but also to modify existing nanostructures at specific locations. The tip of an AFM and the space between the tip and surface structures provide a nanosized environment where researchers can design and perform chemical reactions. With the easy translation of the tip, the position where the chemical event happens can be moved controllably. In this talk, an overview will be provided to summarize recent progresses related to the development of the technique. The creation of metal and conducting polymer nanostructures using electrochemical "dip-pen" nanolithography, the modification of inorganic nanowires and the guided growth of thin conducting polymer nanostructures with controlled geometry will all be discussed.