The invention comprises a system for controlling a charged particle beam shape and direction relative to a controlled and dynamically positioned patient and/or an imaging surface, such as a scintillation plate of a tomography system and/or a first two-dimensional imaging system coupled to a second two-dimensional imaging system. Multiple interlinked beam/patient/imaging control stations allow safe zone operation and clear interaction with the charged particle beam system and the patient. Both treatment and imaging are facilitated using automated sequences controlled with a work-flow control system.