Methods, devices and systems for patterning of substrates using charged particle beams without photomasks and without a resist layer. Material can be removed from a substrate, as directed by a design layout database, localized to positions targeted by multiple, matched charged particle beams. Reducing the number of process steps, and eliminating lithography steps, in localized material removal has the dual benefit of reducing manufacturing cycle time and increasing yield by lowering the probability of defect introduction. Furthermore, highly localized, precision material removal allows for controlled variation of removal rate and enables creation of 3D structures or profiles. Local gas injectors and detectors, and local photon injectors and detectors, are local to corresponding ones of the columns, and can be used to facilitate rapid, accurate, targeted substrate processing.