An apparatus for cleaning the specimen and interior specimen chamber of Transmission Electron Microscopes, and similar electron- or charged-particle-beam instruments consisting of a plasma cleaning device mounted on a hollow rod that replaces the stage through the air lock of the instrument by being the same shape and size as the stage support rod. The plasma cleaning device is a small hollow cathode that is excited by RF power. Air or other oxygen containing mixtures is admitted to the plasma through the hollow rod at a pressure below 1 Torr. The plasma creates oxygen radicals from the oxygen containing gas. The oxygen radicals oxidize the hydrocarbons contamination and convert them to easily pumped gases. The apparatus can be attached to the electron microscope whenever cleaning is needed, and then is easily removed to return the instrument to its analytical function.