In a reactive ion beam etching system, gas phase collision processes in the reaction chamber were identified from the energy distributions of positive ions originating from source plasmas with O2, SF6, and CF4as feed gases. The ion energy distributions are determined by a quadrupole mass spectrometer for main beam energies below 500 eV at typical working pressures in the reaction chamber of 1–10×10−2Pa. Besides near thermal ions a considerable amount of high energy fragmentation products were detected for a number of primary molecular ions. The relative intensities of these products compared to the parent ions suggest a non‐negligible influence of gas phase dissociation processes on the etch or deposition characteristics of molecular ion beams and the resulting properties of surfaces treated under elevated working pressure conditions.