A system for focusing ultrasonic energy through intervening tissue into a target site within a tissue region includes a transducer array including transducer element, an imager for imaging the tissue region, a processor receiving images from the imager to determine boundaries between different tissue types within the intervening tissue and generate correction factors for the transducer elements to compensate for refraction occurring at the boundaries between the tissue types and/or for variations in speed of sound. A controller is coupled to the processor and the transducer array to receive the correction factors and provide excitation signals to the transducer elements based upon the correction factors. The correction factors may include phase and/or amplitude correction factors, and the phases and/or amplitudes of excitation signals provided to the transducer elements may be adjusted based upon the phase correction factors to focus the ultrasonic energy to treat tissue at the target site.