A system for processing biological or other samples includes an array of transducer elements that are positioned to align with sample wells in a microplate. Each transducer element produces ultrasound energy that is focused towards a well of the microplate with sufficient acoustic pressure to cause inertial cavitation. In one embodiment, the transducers are configured to direct ultrasound energy into cylindrical wells. In other embodiments, the transducer elements are configured to direct ultrasound energy into non-cylindrical wells of a microplate.