Methods and apparatus for controlling a gas cluster ion beam formed from a plurality of process gases in a gas mixture. The methods and apparatus involve measuring gas analysis data relating to the composition of the gas mixture and modifying the irradiation of the workpiece in response to the detected parameter. The gas analysis data can be derived from samples of the composition of the gas mixture flowing from a gas source to the gas cluster ion beam apparatus or samples of the residual gases inside the vacuum vessel of the gas cluster ion beam apparatus.