A processing system is provided for irradiating a substrate with a gas cluster ion beam (GCIB). The system includes a vacuum vessel that has an interior and is configured to support the substrate therein, and at least one nozzle for forming and emitting a gas cluster beam. The at least one nozzle is configured to direct the gas cluster beam within the vacuum vessel toward the substrate. An ionizer is positioned to ionize the gas cluster beam to form the GCIB. A main gas supply of the system is in fluid communication with the at least one nozzle for supplying gas to the nozzle. The system also includes a plasma-generating apparatus that communicates with the interior of the vacuum vessel and which is configured to receive a cleaning gas and selectively emit plasma for cleaning the interior of the vacuum vessel.