Functional devices can be directly assembled using microgrippers with an in situ electron microscope. Two simple and compact silicon microgripper designs are investigated here. These are operated by electrothermal actuation, and are used to transfer a catalytically grown multi-walled carbon nanofibre from a fixed position on a substrate to the tip of an atomic force microscope cantilever, inside a scanning electron microscope. Scanning of high aspect ratio trenches using the nanofibre supertip shows a significantly better performance than that with standard pyramidal silicon tips. Based on manipulation experiments as well as a simple analysis, we show that shear pulling (lateral movement of the gripper) is far more effective than tensile pulling (vertical movement of gripper) for the mechanical removal of carbon nanotubes from a substrate.