Provided is a method of controlling a gas cluster ion beam (GCIB) system for processing structures on a substrate. A GCIB system comprises deflection plates for directing a GCIB towards a substrate, the GCIB system coupled to a substrate scanning device configured to move a substrate in three dimensions. The substrate is exposed to the GCIB while the substrate is being moved by the substrate scanning device. A controller is used to control a set of deflection operating parameters comprising a deflection angle φ, voltage differential of the deflection plates, frequency of the deflection plate power, beam current, substrate distance, pressure in the nozzle, gas flow rate in the process chamber, separation of beam burns, duration of the bean burn, and/or duty cycle of the beam deflector output.