A cold field emission (CFE) electron source for a focused electron beam system such as a transmission electron microscope (TEM), scanning transmission electron microscope (STEM), or scanning electron microscope (SEM) is disclosed. The source employs an emitter enclosure electrode behind the CFE tip which, in conjunction with the extractor electrode, defines a closed volume that can be thoroughly cleaned by electron impact desorption (EID) and radiative heating from a heated filament located between the emitter enclosure electrode and extractor electrode. The extractor electrode may have a counterbore which restricts backscattered electrons generated at the extractor from reaching portions of the source and gun which have not been cleaned by EID. Pre-cleaning of the emitter enclosure electrode and extractor electrode prior to cold field emission substantially improves both source emission stability and frequency noise characteristics, enabling source operation over time intervals adequate for application to TEMs, STEMs, and SEMs.