A model for beam customization with collimators and a range-compensating filter based on the phase-space theory for beam transport is presented for dose distribution calculation in the treatment planning of radiotherapy with protons and heavier ions. Independent handling of pencil beams in conventional pencil-beam algorithms causes unphysical collimator-height dependence in the middle of large fields, which is resolved by the framework comprised of generation, transport, collimation, regeneration, range-compensation and edge-sharpening processes with a matrix of pencil beams. The model was verified to be consistent with measurement and analytic estimation at a submillimeter level in the penumbra of individual collimators with a combinational-collimated carbon-ion beam. The model computation is fast, accurate and readily applicable to pencil-beam algorithms in treatment planning with the capability of combinational collimation to make the best use of the beam-customization devices.