A method of using a radiation system having a multileaf collimator ("MLC") to adjust for unevenness in the radiation emitted by the system is disclosed. By appropriately controlling the MLC in accordance with the invention the system can be operated without a flattening filter. In addition, the invention allows the system user to vary the radiation beam energy in the course of a single treatment, without the need to use or change flattening filters. A map of the uneven radiation beam intensity in the treatment area is obtained, and the map information is combined with a treatment plan to control movement of the leaves of the MLC such that each area receives the correct radiation dose.