A system and method for cleaning a substrate, such as a semiconductor wafer, utilizes a rotatable wafer supporting assembly with a cylindrical body to provide stability for the substrate being cleaned, even at high rotational speeds. The rotatable wafer supporting assembly may include wafer holding mechanisms with pivotable confining members that are configured to hold the substrate using centrifugal force when the wafer supporting assembly is rotated. In an embodiment, the cleaning system may include a positioning system operatively connected to an acoustic transducer to provide meaningful control of the acoustic energy applied to a surface of the substrate by selectively changing the distance between the acoustic transducer and the substrate surface so that the substrate can be cleaned more effectively.