A method is disclosed for processing a silicon workpiece including a hybrid thermometer system for measuring and controlling the processing temperature where fabrication materials have been or are being applied to the workpiece. The hybrid thermometer system uses optical reflectance and another thermometer technique, such as a thermocouple and/or a pyrometer. Real-time spectral data are compared to values in a spectrum library to determine the “surface conditions”. A decision is then made based on the surface conditions as to how the temperature is measured, e.g., with optical reflectance, a pyrometer, or a thermocouple, and the temperature is measured using the appropriately selected technique. Utilizing the hybrid thermometer system, the temperature of a silicon workpiece may be accurately measured at low temperatures while accounting for the presence of fabrication materials.