The invention comprises a patient positioning and/or repositioning system, such as a laying, semi-vertical, or seated patient positioning, alignment, and/or control method and apparatus used in conjunction with multi-axis charged particle radiation therapy. Patient positioning constraints optionally include one or more of: a seat support, a back support, a head support, an arm support, a knee support, and a foot support. One or more of the positioning constraints are preferably movable and/or under computer control for rapid positioning, repositioning, and/or immobilization of the patient. The system optionally uses an X-ray beam that lies in substantially the same path as a proton beam path of a particle beam cancer therapy system. The generated image is usable for: fine tuning body alignment relative to the proton beam path, to control the charged particle beam path to accurately and precisely target the tumor, and/or in system verification and validation.