<p>Aspects of the invention generally provide an apparatus and method for processing substrates using a multi-chamber processing system that is adapted to process substrates and analyze the results of the processes performed on the substrate. In one aspect of the invention, one or more analysis steps and/or precleaning steps are utilized to reduce the effect of queue time on device yield. In one aspect of the invention, a system controller and the one or more analysis chambers are utilized to monitor and control a process chamber recipe and/or a process sequence to reduce substrate scrap due to defects in the formed device and device performance variability issues. Embodiments of the present invention also generally provide methods and a system for repeatably and reliably forming semiconductor devices used in a variety of applications.</p>
