Contamination may be removed from an emitter tip of a field emitter during operation of the emitter tip in a system having an electron beam column having an electrode with a beam defining aperture, an electron collector located proximate to the beam defining aperture between the electrode and the field emitter, and an electron deflector located between the emitter tip and the electron collector. At regular predetermined intervals an electron beam from the emitter tip may be deflected away from a path through the beam defining aperture and onto the electron collector. An electron beam current to the electron collector may be determined and the emitter tip may be flash heated if the current to the electron collector is below a threshold.