It has long been the bane of analytical electron microscopy (AEM) that the use of focused probes during microanalysis of specimens increases the local rate of hydrocarbon contamination. This is most succinctly observed by the formation of contamination deposits (fig.l) during focused probe work typical of AEM studies. While serving to indicate the location of the electron probe, the contamination obliterates the area of the specimen being analyzed and adversely affects all quantitative microanalysis methodologies. A variety of methods including: UV, electron beam flooding, heating and/or cooling can decrease the rate of contamination, however, none of these methods directly attack the source of specimen borne contamination . Research has shown that reactive gas plasmas may be used to clean both the specimen and stage for AEM, in this study we report on quantitative measurements of the reduction in contamination rates in an AEM as a function of operating conditions and plasma gases.