A polymer inactivation method for a polycrystalline silicon manufacturing device, wherein the polymer byproducts are treated and additionally treated in a manner that controls the rate of reaction. The polymer byproducts are treated with a first inert gas under partial vacuum and a second oxygen containing gas to convert the polymer byproducts. The reaction rate can be controlled by regulating the fill pressure of reactant gas, controlling the amount of oxygen in the reactant gas, and stripping of the raw polymer with heat and or a vacuum. The solid byproduct remaining after treating the polymer, which is predominately silicon suboxides (SiOx) and silicon dioxide (SiO2), is inert and is easily removed.