A luminescence-guided focused ultrasound apparatus, comprising at least one focused ultrasound transducer that delivers focused ultrasound energy to at least one focal region within the subject, at least one luminescence detector that detects a luminescence signal generated within the subject, and at least one guiding element that guides the at least one focused ultrasound transducer to deliver focused ultrasound energy to the at least one focal region wherein the at least one guiding element is influenced by the detected luminescence signal. The at least one focused ultrasound transducer may be configured in operate in a plurality of modes, including a low-intensity mode for delivering low-intensity focused ultrasound energy and a high-intensity mode for delivering high-intensity focused ultrasound energy.