When constructing compensators for radiation therapy using ion or proton radiation beams, a computer-aided compensator editing method includes overlaying an initial 3D compensator model on an anatomical image of a target mass (e.g., a tumor) in a patient, along with radiation dose distribution information. A user manipulates pixels or voxels in the compensator model on a display, and a processor automatically adjusts the dose distribution according to the user edits. The user iteratively adjusts the compensator model until the dose distribution is optimized, at which time the optimized compensator model is stored to memory and/or output to a machining device that constructs a compensator from the optimized model.