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In this paper, a focused ion beam processing technique is presented that facilitates the modification of carbon nanotubes (CNTs) in terms of length, diameter, and orientation. The CNTs are mounted onto an atomic force microscope (AFM) probe by using a nanorobotic microgripper-based pick-and-place handling strategy. Such CNT-enhanced AFM probes are needed for metrology measurements of nanostructures with critical dimensions and high aspect ratios. The complete process of assembly and processing is realized inside a nanorobotic dual beam scanning electron microscope (SEM) and focused ion beam (FIB) machine.