Multi-pixel electron microbeam irradiator systems and methods are provided with particular applicability for selectively irradiating predetermined cells or cell locations. A multi-pixel electron microbeam irradiator system can include a plurality of individually addressable electron field emitters sealed in a vacuum. The multi-pixel electron microbeam irradiator system can include an anode comprising one or more electron permeable portions corresponding to the plurality of electron field emitters. Further, the multi-pixel electron microbeam irradiator system can include a controller operable to individually control electron extraction from each of the electron field emitters for selectively irradiating predetermined locations such as cells or cell locations.