A system for performing single wavelength ellipsometry (SWE) on a thin film on a multi-layer substrate such as silicon-on-insulator (SOI) applies a measurement beam having an absorption distance less than the thickness of the superficial layer of the multi-layer substrate. For example, for an SOI substrate, the measurement beam is selected to have a wavelength that results in an absorption distance that is less than the superficial silicon layer thickness. The system can include a cleaning laser to provide concurrent cleaning to enhance measurement accuracy without negatively impacting throughput. The measurement beam source can be configured to provide a measurement beam at one wavelength and a cleaning beam at a longer wavelength, so that the absorption depth of the measurement beam is less than the superficial layer thickness while the absorption depth of the cleaning beam is greater than the superficial layer thickness.