Methods and systems for direct atomic layer etching and deposition on or in a substrate using charged particle beams. Electrostatically-deflected charged particle beam columns can be targeted in direct dependence on the design layout database to perform atomic layer etch and atomic layer deposition, expressing pattern with selected 3D-structure. Reducing the number of process steps in patterned atomic layer etch and deposition reduces manufacturing cycle time and increases yield by lowering the probability of defect introduction. Local gas and photon injectors and detectors are local to corresponding columns, and support superior, highly-configurable process execution and control.