They used either electron beam lithography or ion-beam etching. You basically use an electron microscope to write instead of look, by allowing the beam of electrons to do the damage that you would normally try to prevent by scanning quickly over the surface.
Alternately, you can do the same thing by steering a beam of high-energy ions (usually Ga+ or charged buckminsterfullerene) with magnetic fields.
Alternately, you can do the same thing by steering a beam of high-energy ions (usually Ga+ or charged buckminsterfullerene) with magnetic fields.