Electron beam lithography for direct writing ICs has been around for decades. Put down a layer of resist, expose with a steered electron beam. It works fine, down to at least 7nm, but it's slow. It's never been cost effective for making ICs, except for occasional one-offs. It's mostly used to make masks.
Sure. Heidelberg's recently made [1] some cool tools ("maskless aligners") that can expose a ≈150mm wafer in an hour or so down to ≈500nm resolution, which is very convenient when rapidly iterating through one-off low-resolution designs or something in a research lab (for comparison, electron beam lithography does the same to ≈10nm resolution in maybe a day). It's still part of the whole fabricate-everything-as-2D-layers-on-a-wafer paradigm, though, and has the same limitations (e.g., temperature limits) as standard silicon circuitry made with conventional photolithography.
