The present invention generally provides an apparatus and method of processing substrates to uniformly remove any residual contamination from the surface of a substrate by use of an appropriate cleaning chemistry and contact with a cleaning medium. In one embodiment, the cleaning medium, such as is a brush or a scrubbing component that is positioned in a cleaning module. In one embodiment, the process of cleaning the surface of a substrate W is completed by “scrubbing” the surface of the substrate while using a cleaning solution that is selected to chemically etch a material from the surface of the substrate. In one aspect, the amount of material removed from the surface of a substrate is only about 10-30 Angstroms (Å). In one embodiment, the substrate surface is cleaned by use of a scrubbing process that uses a fluid that doesn't react with the exposed materials on the surface of the substrate. The fluid is thus used to lubricate the surfaces in contact and to carry any abraded material away from the surface of the substrate. In one aspect, the fluid may be DI water. In one aspect, it may be desirable to add ultrasonic or megasonic agitation to the substrate during the cleaning process to help remove or dislodge material from the surface of the substrate.