An apparatus and method for automatically lysing a clot to recanalize vessels using ultrasound, with or without nanoparticles, microbubbles, thrombolytic drugs or other agents, is described herein. At least one ultrasound transducer with a specified geometry, bandwidth and/or transmit pulse characteristics can generate a more uniform 3-dimensional volume of defocused acoustic energy into a target area of the body. When an agent (such as, but not limited to, microbubbles) is used to lyse a clot, a certain level of ultrasound energy may be desired in order to effect certain actions or states of the agent. Bone attenuation may present an issue inhibiting sufficient ultrasound energy from reaching the agent in order to attain the desired agent action. The relative patient dimensions and location of the clot may also present an issue.