A method of operating an ion beam system comprising a voltage supply system, an acceleration electrode (13, 27) and first (51e, 52e), second (51d, 52d), third (51c, 52c), fourth (51b, 52b) and fifth (51a, 52a) pairs of deflection electrodes distributed along an ion beam path, wherein the pairs of deflection electrodes each have a first electrode (51a, 51b, 51c, 51d, 51e) disposed on a first side of the ion beam path and a second electrode (52a, 52b, 52c, 52d, 52e) disposed on a second side of the ion beam path, opposite to the first side; wherein the method comprises accelerating ions of the ion beam to a low, medium, or high kinetic energy to traverse said pairs of deflection electrodes with the respective kinetic energy, by selecting a respective mode of operation of the voltage supply system; wherein the method further comprises: in a first mode of operation, deflecting the ion beam by applying voltages to the fourth and fifth pairs of deflection electrodes such that the voltages applied to the first and second electrodes of each of the fourth and fifth pairs have opposite polarity and such that the voltage ("+") applied to the first electrode of the fourth pair and the voltage ("-") applied to the first electrode of the fifth pair have opposite polarity, while supplying the electrodes of the first, second and third pairs (51e, 52e, 51d, 52d, 51c, 52c) with a potential such that they do not deflect the ion beam; in a second mode of operation, deflecting the ion beam by applying voltages to the second, third, fourth and fifth pairs of deflection electrodes such that the voltages applied to the first and second electrodes of each of the second, third, fourth and fifth pairs have opposite polarity and such that the voltage ("+") applied to the first electrodes (51d, 51c) of the second and third pairs and the voltage ("-") applied to the first electrodes (51b, 51a) of the fourth and fifth pairs have opposite polarity, while supplying the electrodes of the first pair (51e, 52e) with a potential such that they do not deflect the ion beam; and in a third mode of operation, deflecting the ion beam by applying voltages to the first, second, third, fourth and fifth pairs of deflection electrodes such that the voltages applied to the first and second electrodes of each of the first, second, third, fourth and fifth pairs have opposite polarity and such that the voltage ("+") applied to the first electrodes (51e, 51b) of the first and second pairs and the voltage ("-") to the first electrodes (51c, 51d, 51e) of the third, fourth and fifth pair have opposite polarity, wherein the first, second, and third modes of operation are used for ions having the low, medium, or high kinetic energy, such as 1 keV, 10 keV, or 30 keV, respectively. in a first mode of operation, deflecting the ion beam by applying voltages to the fourth and fifth pairs of deflection electrodes such that the voltages applied to the first and second electrodes of each of the fourth and fifth pairs have opposite polarity and such that the voltage ("+") applied to the first electrode of the fourth pair and the voltage ("-") applied to the first electrode of the fifth pair have opposite polarity, while supplying the electrodes of the first, second and third pairs (51e, 52e, 51d, 52d, 51c, 52c) with a potential such that they do not deflect the ion beam; in a second mode of operation, deflecting the ion beam by applying voltages to the second, third, fourth and fifth pairs of deflection electrodes such that the voltages applied to the first and second electrodes of each of the second, third, fourth and fifth pairs have opposite polarity and such that the voltage ("+") applied to the first electrodes (51d, 51c) of the second and third pairs and the voltage ("-") applied to the first electrodes (51b, 51a) of the fourth and fifth pairs have opposite polarity, while supplying the electrodes of the first pair (51e, 52e) with a potential such that they do not deflect the ion beam; and in a third mode of operation, deflecting the ion beam by applying voltages to the first, second, third, fourth and fifth pairs of deflection electrodes such that the voltages applied to the first and second electrodes of each of the first, second, third, fourth and fifth pairs have opposite polarity and such that the voltage ("+") applied to the first electrodes (51e, 51b) of the first and second pairs and the voltage ("-") to the first electrodes (51c, 51d, 51e) of the third, fourth and fifth pair have opposite polarity, wherein the first, second, and third modes of operation are used for ions having the low, medium, or high kinetic energy, such as 1 keV, 10 keV, or 30 keV, respectively.