A method of temperature control for selenization process conducted in vacuum quartz tube furnace with radial energy transfer and a movable sample holder has been described. Selenization of metallic precursors to obtain CuInSe 2 absorber layer of a photovoltaic cell requires a special approach to the temperature regulation, where two-stage heating process is necessary. The modular process control system was developed in which the first module playing a supervising role was built in LabVIEW environment and the second one, called a predictor, was built in MATLAB. Relatively quick movement of the holder from the cold to the hot regions of the furnace allows for a rapid change of sample temperature, typical of rapid thermal processing processes.