The self-organization of supramolecular structures, in particular gold-containing hydrogen-bonded rosettes, on highly oriented pyrolytic graphite (HOPG) surfaces was investigated by tapping-mode atomic force microscopy (TM-AFM) and scanning tunneling microscopy (STM). TM-AFM and high-resolution STM results show that these hydrogen-bonded assemblies self-organize to form highly ordered domains on HOPG surfaces. We find that a subtle change in one of the building blocks induces two different orientations of the assembly with respect to the surface. These results provide information on the control over the construction of supramolecular nanoarchitectures in 2D with the potential for the manufacturing of functional materials based on structural manipulation of molecular components.