A system and methods are provided and thrombi treatments in which hyperthermia is induced in an initial phase and cavitation and/or drug release are induced in a subsequent phase in a region of interest in a human or animal body. The system includes an energy transmitter having a variable intensity and/or a variable frequency and a control unit arranged to control the energy transmitter to operate in at least two different modes. In one embodiment, the first mode is a mode of operation having a mechanical index below a threshold level for cavitation and the second mode is a mode of operation having a mechanical index above a threshold level for cavitation. In another embodiment, the first mode induces hyperthermia below a temperature threshold for releasing an encapsulated agent and the second mode induces hyperthermia above the temperature threshold. The initial hyperthermia treatment enhances the effect of subsequent treatments.
