A multi-scale manufacturing system comprising a centrally located multi-axis and multi-dimensional first manipulating component associated with a housing for manipulating a substrate and a template, a control subsystem coupled to the first manipulating component for controlling movement thereof, a pre-alignment subsystem for pre-aligning the substrate and the template, an assembly station for applying nanomaterial to the template, an alignment station for aligning the template and the substrate together to form a workpiece assembly, and a transfer subsystem for applying pressure to the workpiece assembly for transferring the nanomaterial from the template to the substrate.