Atomic force microscopy (AFM) reveals that the nanoscopic surface topography, and growth and dissolution mechanisms of molecular crystals are correlated with intermolecular bonding in the solid state. The orientation and growth of topographical features such as steps, ledges and kinks are primarily a manifestation of the enthalpically favored bonding directions within a given crystallographic plane. Hydrogen bonded crystals and charge transfer salts, which exhibit anisotropic solid state bonding, were found to have analogous topographical motifs in terms of surface features oriented along primary bonding directions. The role of these surface features, particularly ledges, in directing the nucleation and growth of secondary crystalline materials is described. Facile nucleation and oriented crystal growth is observed on substrate ledge sites, behavior that is attributed to lowering of the prenucleation aggregate free energy via "ledge directed epitaxy." This involves a lattice match between the substrate and growing phase along the ledge direction, and equivalent dihedral angles of the substrate ledge sites and a pair of aggregate planes whose identity is assigned on the basis of the structure of the mature crystal.