In a charged particle or electron beam system, gas, such as argon or helium, is introduced over the surface of a substrate and ionized to neutralize charge accumulating on the surface from interactions caused by the impinging charged particles. The gas can be distributed throughout the gas chamber or confined to an area above the substrate. The radiation beam to ionize the gas can be directed across or towards the surface of the substrate. In the latter case, the gas pressure may be reduced to zero.