The molecular self-assembly of several molecular species on Cu(111) has been studied with ultra-high vacuum scanning tunneling microscopy. A coexistence of small flower and interlocking pinwheel structure is observed for the self-assembly of phenyl-propynenitrile molecules, with the preference of the more complex pinwheel structure attributed to the surface stress induced by molecular adsorption. Metal-organic coordination interaction on a 2-dimensional surface has been explored through a comparative study of isocyanide and cyanide molecules with the same molecular backbones. And the effects of confinement into the self-assembled anthraquinone cavities has been demonstrated.