A method of reducing atom ejection from a sample during electron beam bombardment. An electron beam is directed through a low pressure environment toward a surface of the sample. The electron beam thereby impinges on the sample at a target location, and thereby causes characteristic x-ray emission from the target location of the sample. A capping precursor is introduced into the low pressure environment, where the capping precursor forms a capping layer on the surface of the sample at the target location when contacted by the electron beam. The capping layer thereby reduces atom ejection from the sample at the target location, while not appreciably impeding and confounding the characteristic x-ray emission from the target location of the sample.