A method of cleaning calibration and other substrates that improves the correlation of measurements from calibration and product substrates and increases the useful life of the calibration substrates is herein disclosed. By exposing a calibration substrate to ultraviolet light, a reaction is triggered that results in the cleaning of the contaminants from the calibration substrate. For instance, monatomic oxygen is introduced to contaminants on the surface of a calibration substrate to remove the contaminants without inducing modifications in the substrate itself. Through the cleaning process, the temperature of the calibration substrate may be controlled to limit adverse effects caused by the overheating of the calibration substrate.