A reactor for processing a substrate includes a first housing defining a processing chamber and supporting a light source and a second housing rotatably supported in the first housing and adapted to rotatably support the substrate in the processing chamber. A heater for heating the substrate is supported by the first housing and is enclosed in the second housing. The reactor further includes at least one gas injector for injecting at least one gas into the processing chamber onto a discrete area of the substrate and a photon density sensor extending into the first housing for measuring the temperature of the substrate. The photon density sensor is adapted to move between a first position wherein the photon density sensor is directed to the light source and a second position wherein the photon density sensor is positioned for directing toward the substrate. Preferably, the communication cables comprise optical communication cables, for example sapphire or quartz communication cables. A method of processing a semiconductor substrate includes supporting the substrate in a sealed processing chamber. The substrate is rotated and heated in the processing chamber in which at least one reactant gas is injected. A photon density sensor for measuring the temperature of the substrate is positioned in the processing chamber and is first directed to a light, which is provided in the chamber, for measuring the incident photon density from the light and then repositioned to direct the photon density sensor to the substrate to measure the reflection of the light off the substrate. The incident photon density is compared to the reflected light to calculate the substrate temperature.