The current invention includes methods and apparatuses for processing, that is, altering and imaging, a sample in a high pressure charged particle beam system. Embodiments of the invention include a cell in which the sample is positioned during high pressure charged particle beam processing. The cell reduces the amount of gas required for processing, thereby allowing rapid introduction, exhaustion, and switching between gases and between processing and imaging modes. Maintaining the processes gases within the cell protects the sample chamber and column from contact with the gases. In some embodiments, the temperature of the cell walls and the sample can be controlled.