1. A non-transitory tangible medium having treatment planning software stored thereon, said software comprising one or more algorithms for optimizing a treatment plan in stages according to a preprogrammed schedule based on an objective function including patient specific information, said software having an interactive mode, wherein said interactive mode comprises: code for holding the optimization process at a user-selected stage until receiving user instructions; code for accepting user adjustments to the objective function while the optimization process is underway; and code for restarting the optimization at a user-selected stage after adjustments have been made to the objective function.