We present here a polysilicon electrothermal microfabricated nanogripper capable of manipulating nanowires and nanotubes in the sub-100 nm range. The nanogripper was fabricated with a mix and match microfabrication process, combining high throughput of photolithography with 10 nm resolution of electron beam lithography. Vertically grown III–V nanowires with a diameter of 70 nm were picked up using the nanogripper, allowing direct transfer of the nanogripper-nanowire ensemble into a transmission electron microscope (TEM) for structural characterization. By refining the end-effectors with focused ion beam milling and subsequently coating these with Au, the nanogripper could lift up laterally aligned single-walled carbon nanotubes from a 1 µm wide trench, while immediately making good electrical contact. One such carbon nanotube was structurally and electrically characterized real-time in TEM, showing a breakdown current density of approximately 0.5 × 1012Am−2. The nanogripper is the smallest microfabricated gripper to date and is the first tool showing repeatable, 3D nanomanipulation of sub-100 nm structures.