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This paper presents a new method to assemble individual nanostructures such as a single strand carbon nanotube (CNT) at a deterministic location of MEMS devices. An array of vertically aligned CNTs grown on nickel nano-dots was encapsulated into MEMS scale polymer blocks that were then transplanted to MEMS cantilevers to make CNT-tipped atomic force microscope (AFM) probes. Even manual transfer of a CNT-bearing polymer block to the target location leads to reliable and reproducible fabrication of a CNT-based device such as the CNT-tipped AFM probe. The scanning experimental results on AFM standard gratings and biological samples confirm the superior characteristic of CNTs (high aspect ratio and toughness) and justify this assembly method can be useful to mass produce nanostructured MEMS devices.