Disclosed herein are techniques directed toward a protective shutter for a charged particle microscope. An example apparatus at least includes a charged particle column and a focused ion beam (FIB) column, a gas injection nozzle coupled to a translation device, the translation device configured to insert the gas injection nozzle in close proximity to a stage, and a shutter coupled to the gas injection nozzle and arranged to be disposed between the sample and the SEM column when the gas injection nozzle is inserted in close proximity to the stage.