The higher-speed implementation and higher integration of electronic equipment gives increasingly higher importance to high-accuracy super-fine machining technology. A developed ion beam milling machine, which responds to this requirement, is a useful means to implement the higher performance of electronic equipment. The machine compactly comprises a large scale ion source that has been developed by the application of the essence of neutral beam injection equipment for heating plasma in nuclear fusion facilities, and a water cooled substrate holder that is capable of simultaneously treating up to 16 substrates and is rotated and revolved at any gradient angle with respect to the beam. The large scale ion source is used to generate uniform beams at low divergence angles. The result is that high accuracy and the highest throughput unheard of can be achieved with machining deviations at ± 3% or less.