An environmental cell for a charged particle beam system allows relative motion between the cell mounted on an X-Y stage and the optical axis of the focusing column, thereby eliminating the need for a sub-stage within the cell. A flexible cell configuration, such as a retractable lid, permits a variety of processes, including beam-induced and thermally-induced processes. Photon yield spectroscopy performed in a charged particle beam system and using gas cascade amplification of the photoelectrons allows analysis of material in the cell and monitoring of processing in the cell. Luminescence analysis can be also performed using a retractable minor.