The invention comprises a system for patient specific control of charged particles in a charged particle beam path using one or more trays inserted into the charged particle beam path, such as at the exit port of a gantry nozzle in close proximity to a tumor of a patient. Each tray holds an insert, such as a patient specific insert for controlling the energy, focus depth, and/or shape of the charged particle beam. Examples of inserts include a range shifter, a compensator, an aperture, a ridge filter, and a blank. Trays in a tray assembly are optionally retracted into an output nozzle of a charged particle cancer treatment system. Optionally and preferably, each tray communicates a held and positioned insert to a main controller of the charged particle cancer therapy system.