A plasma processing method and apparatus are disclosed in which a low energy, high frequency plasma is utilized to remove both amorphous damage resulting from various specimen preparation techniques and contamination, mainly in form of hydrocarbons, from transmission electron microscopy specimens and specimen holders. The system comprises a vacuum system, a plasma chamber into which the specimen and the specimen holder are inserted, a housing having an access port with removable inner sleeve components, and a high frequency power supply which is coupled to the plasma chamber and enables both the generation and maintenance of the plasma. The inner sleeve components are preferably capable of accepting specimen holders produced by all manufacturers of transmission electron microscopes. In the preferred embodiment, the vacuum system comprises an oil-free vacuum system. To commence processing, the vacuum system is engaged for the evacuation of the plasma chamber for subsequent formation of the plasma. Processed gas may be introduced into the plasma chamber through the automated operation of various switches and valves. The plasma formation is preferably initiated through the coupling of an oscillating field to the plasma chamber. Many processed gas mixtures can be used. The preferred processed gas mixture comprises a mixture of twenty-five percent oxygen and seventy-five percent argon. The oxygen chemically reacts with hydrocarbons on the specimen and specimen holder and converts them to CO.sub.2 and H.sub.2 O. The argon provides the means to reduce specimen amorphous damage.