A method for controlled deposition and orientation of molecular sized nanoelectromechanical systems (NEMS) on substrates is disclosed. The method comprised: forming a thin layer of polymer coating on a substrate; exposing a selected portion of the thin layer of polymer to alter a selected portion of the thin layer of polymer; forming a suspension of nanostructures in a solvent, wherein the solvent suspends the nanostructures and activates the nanostructures in the solvent for deposition; and flowing a suspension of nanostructures across the layer of polymer in a flow direction; thereby: depositing a nanostructure in the suspension of nanostructures only to the selected portion of the thin layer of polymer coating on the substrate to form a deposited nanostructure oriented in the flow direction. By selectively employing portions of the method above, complex NEMS may be built of simpler NEMSs components.