In the present study, 1-dodecanethiol self-assembled monolayers (SAMs) on graphene oxide (GO) –Au (Gold) thin films as molecular templates for the selective deposition of multilayer films was performed. Thus, heterostructured GO/Au/DDT and DDT/Au/GO thin film are fabricated by sputtering Au target onto modified GO structure or self-assembled 1-dodecanethiol (DDT) arrays. It has been shown that a new device concept can be made by completing the glass substrate with the surface heterostructures; i.e. layer GO sheet or DDT with Au nanoparticles (Au NPs). In the light of the performed study, the layer-by-layer assembling of DDT on the GO sheet-Au thin films template has been proved for the distinct conjugation. Also, Optical and morphological characterizations are coherent with the instantaneous nucleation and growth model over the modified DDT-Au NPs-GO or GO-Au NPs-DDT thin films in the aspect of surface roughness, the phonon transport, and other multilayer films properties. As a consequence, the multilayer films of DDT-capped Au thin films and GO sheets have shown a better hybrid nanostructure with higher consistency, hierarchy and surface area. In addition, this work will present a new perspective for template preparation based on nanostructured thin films due to its unique properties resulting from nanoscale properties.