A method of operating a filament assisted chemical vapor deposition (FACVD) system. The method includes depositing a film on a substrate in a reactor of the FACVD system. During the depositing, a DC power is supplied to a heater assembly to thermally decompose a film forming material. The method also includes cleaning the heater assembly, or an interior surface of the reactor, or both. During the cleaning, an alternating current is supplied to the heater assembly to energize a cleaning media into a plasma.