A nanostructure is fabricated using charged particle deposition to deposit a catalyst on a substrate. A charged particle beam is directed to location on the substrate where the catalyst is to be deposited, with a beam-activated precursor gas also being directed to the location. For example, a nickel dot can be selectively deposited onto a substrate by using a charged particle beam to decompose a nickel-containing precursor gas, and then a carbon nanotube can be grown on the nickel dot, with the diameter of the nanotube conforming to the size of the nickel dot.