Abstract: A cleaning system for use with a micro-column array, electron beam lithography system is described. The cleaning system includes an oxidizer source and an oxidizer distribution mechanism that introduces an oxidizer into the imaging chamber of the lithography system. The oxidizer is pumped into the chamber at a flow rate and pressure that maintains a required sub-atmospheric pressure within the imaging chamber. The oxidizer acts to oxidize carbon contamination that may be present in the imaging chamber or on the surfaces of components within the chamber, such as the imaging mask. A volatile oxidized carbon gas is produced by the oxidization of the carbon contaminants. The oxidized carbon gas is pumped out of the imaging chamber to thereby remove the carbon contamination from the chamber.