One aspect of the present invention relates to a system and method of monitoring for defects on a wafer before and after forming a photoresist layer on the wafer. The system includes a device fabrication system comprising one or more wafer processing system components for producing a device; a defect metrology system integrated within and on track with the fabrication system operative to inspect the wafer for defects before it proceeds to photoresist processing; and a wafer cleaning system for reducing an amount of defects detected on the front and/or back side of the wafer. If the amount of defects have been sufficiently reduced, the front side of the wafer may be coated with a photoresist. Subsequently, the back side of the wafer may be inspected and cleaned while protecting the front side from damage. Cleaning of the wafer may be performed with a thermal shock treatment, for example.