A method of operating a hydrocarbon material processing system includes feeding a hydrocarbon feedstock from a hydrocarbon feedstock source into a reaction tube positioned within an opening of a waveguide, feeding a process gas from a process gas source into the reaction tube, receiving microwaves in the waveguide from a microwave generator, energy from the waveguide in the reaction tube to cause the feedstock and process gas to react and form into a product stream comprising a fuel product. The method also includes periodically delivering a cleaning gas into the reaction tube, without stopping the propagation of the energy and without pausing the feeding of the hydrocarbon feedstock and the process gas into the reaction tube.