This focus review describes a brief overview of our recent achievements on the fabrication of self-assembled nanostructures and following transformation by external stimuli, such as thermal treatment, metal coordination and ultraviolet irradiation. Some stimuli-responsive organic molecules possessing alkyl tails working as adsorption and interaction sites were synthesized to allow the spontaneous formation of various two-dimensional (2D) nanopatterns on a highly oriented pyrolytic graphite (HOPG). The 2D molecular arrangements were investigated by using scanning tunneling microscopy at HOPG/1-phenyloctane interface.