A gas cluster ion beam (GCIB) processing system using multiple nozzles for forming and emitting at least one GCIB and methods of operating thereof are described. The GCIB processing system may be configured to treat a substrate, including, but not limited to, doping, growing, depositing, etching, smoothing, amorphizing, or modifying a layer thereupon. Furthermore, the GCIB processing system may be operated to produce a first GCIB and a second GCIB, and to irradiate a substrate simultaneously and/or sequentially with the first GCIB and second GCIB.