Substrate preparation systems comprising multi-zone cascade brush scrubbers having sonic assemblies disposed between one or more of the scrubber zones for cleaning of disk-shaped substrates, including silicon wafers and disks for data storage devices, such as hard disk drives (HDD), compact discs (CD) and digital video discs (DVD). The system method combines a sonic particle dislodgement/removal assembly into a cascade brush scrubber line comprising a longi-tudinal array of brush pairs in which the substrates process through preparation zones defined by each pair of brushes, the substrates being transited longitudinally through the zones while rotating on an axis normal to their faces. Piezoelectric transducer arrays transmit sound energy to one or both face(s) of the substrate to dislodge and/or remove particles, and the scrubber simultaneously or thereafter sweeps away the particulates. The sonic energy may be ultrasonic, megasonic, or both, applied to the substrate surface(s) in alternating or sequential process steps.