Abstract: A method and a system for manufacturing two-dimensional and three-dimensional nanostructures and nanodevices are described, wherein the formation of the nanostructure (of the nanodevice) on a target substrate is made, at a millimetric or super-millimetric distance from the substrate, by the deposition of material emitted in the form of an atomic/molecular beam having a selected pattern corresponding, at an enlarged scale, to the desired pattern of the nanostructure (nanodevice). The projection of the patterned beam through a diaphragm, associated with the substrate at a micrometric or sub-micrometric distance and having at least one shaped aperture of nanometric size, brings about the formation of a nanostructure pattern which is a convolution of the patterned beam with the diaphragm aperture.