An ion therapy dose planning system comprising: a memory containing: an anatomical patient image; beam configuration data; at least one 3D model of a compensator (22, 62) comprising a plurality of compensator pixels having compensator pixel data, wherein the value of each compensator pixel represents the compensator thickness at each compensator pixel; a processor in communication with the memory via a bus; a graphical user interface including a display and a user input device; wherein the processor executes computer-executable instructions stored in the memory, the instructions including: computing a radiation dose distribution map for ion beam radiation passing through the at least one model of the compensator (22, 62) using beam configuration data; displaying on the display, to a user, a projection of the 3D model of the compensator (22, 62) on the anatomical image of the patient, and the radiation dose distribution map in a beam's eye view representation; receiving user input from the user input device comprising at least one dose distribution objective selected from the group i) intensity range ii) uniformity of intensity and iii) intensity as a biological equivalent effect for at least a region of a patient; receiving user input from the user input device comprising edits to the value of at least one compensator pixel in the beam's eye view representation; generating an optimized 3D model of the compensator (22, 62) by adjusting at least one beam configuration parameter selected from the group i) range ii) modulation iii) margins iv) beam energy based on the user input; and storing the optimized 3D model of the compensator to the memory or computer-readable storage medium. a memory containing: an anatomical patient image; beam configuration data; at least one 3D model of a compensator (22, 62) comprising a plurality of compensator pixels having compensator pixel data, wherein the value of each compensator pixel represents the compensator thickness at each compensator pixel; an anatomical patient image; beam configuration data; at least one 3D model of a compensator (22, 62) comprising a plurality of compensator pixels having compensator pixel data, wherein the value of each compensator pixel represents the compensator thickness at each compensator pixel; a processor in communication with the memory via a bus; a graphical user interface including a display and a user input device; wherein the processor executes computer-executable instructions stored in the memory, the instructions including: computing a radiation dose distribution map for ion beam radiation passing through the at least one model of the compensator (22, 62) using beam configuration data; displaying on the display, to a user, a projection of the 3D model of the compensator (22, 62) on the anatomical image of the patient, and the radiation dose distribution map in a beam's eye view representation; receiving user input from the user input device comprising at least one dose distribution objective selected from the group i) intensity range ii) uniformity of intensity and iii) intensity as a biological equivalent effect for at least a region of a patient; receiving user input from the user input device comprising edits to the value of at least one compensator pixel in the beam's eye view representation; generating an optimized 3D model of the compensator (22, 62) by adjusting at least one beam configuration parameter selected from the group i) range ii) modulation iii) margins iv) beam energy based on the user input; and storing the optimized 3D model of the compensator to the memory or computer-readable storage medium. computing a radiation dose distribution map for ion beam radiation passing through the at least one model of the compensator (22, 62) using beam configuration data; displaying on the display, to a user, a projection of the 3D model of the compensator (22, 62) on the anatomical image of the patient, and the radiation dose distribution map in a beam's eye view representation; receiving user input from the user input device comprising at least one dose distribution objective selected from the group i) intensity range ii) uniformity of intensity and iii) intensity as a biological equivalent effect for at least a region of a patient; receiving user input from the user input device comprising edits to the value of at least one compensator pixel in the beam's eye view representation; generating an optimized 3D model of the compensator (22, 62) by adjusting at least one beam configuration parameter selected from the group i) range ii) modulation iii) margins iv) beam energy based on the user input; and storing the optimized 3D model of the compensator to the memory or computer-readable storage medium.