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We succeeded in integrating individual, pre-existing nanostructures into functional devices using ultrahigh vacuum dynamic nanostenciling and show working devices based on single-walled carbon nanotubes, a benchmark nanomaterial, and porphyrin J-aggregates, a “soft” supramolecular nanomaterial. Nanostructures are first located via atomic force microscopy, while device elements are added step by step, with an achieved positional accuracy of 20 nm, using a shadow mask assembly that moves while being exposed to evaporated material. Electronic transport, potentiometry, and scanning Kelvin probe were used for control at any fabrication stage and were available in situ. Such complex fabrication/characterization capabilities, applicable repeatedly, reliably, and nondestructively, pave the way for dynamic nanostenciling instrumentation to establish itself as a viable tool for easy integration and prototyping of fragile nanostructures synthesized through a wide range of processes. [ABSTRACT FROM AUTHOR]