A radiation treatment planning system and method for generating plans to treat plural target volumes, each associated with a prescribed dose, does not require delivery of radiation to every target volume from every beam direction. Allowing target volumes to be omitted for some control points facilitates generation of treatment plans that deliver less radiation dose to non-target tissues by allowing beam shaping to more closely fit the remaining target volumes. Simulated annealing using an objective function may be applied to determine parameters such as the number of control points for which a target volume is not targeted.