A silicon-containing film on a substrate is subjected to a plasma process using a process gas containing fluorine and carbon, and is thereafter subjected to plasma process using an ammonia gas, whereby ammonium silicofluoride having toxicity and hygroscopic property is adhered to the substrate. The harmful ammonium silicofluoride is removed by the inventive method. After conducting the plasma process using an ammonia gas, the substrate is heated to a temperature not lower than the decomposition temperature of the ammonium silicofluoride to decompose the ammonium silicofluoride in a process container in which the plasma process was conducted, or in a process container connected with the processing vessel which the plasma process was conducted therein and is isolated from a clean room atmosphere.