An important component in the basic chemical and physical mechanisms which govern etching and deposition processes in high density plasmas is the chemical identity and relative fluxes of ionic species at the substrate surface. Here we report line of sight measurements of relative ion fluxes made with a quadrupole mass spectrometer through an orifice in the substrate holder of an electron cyclotron resonance reactor configured for fluorine‐based etching. The relative ion fluxes versus microwave power and pressure for CF4 and CHF3 plasmas have been studied. These data have been compared with Si and SiO2 etch rates to determine the effect of ion flux composition changes on etching processes. It was observed that the F+ ion flux increases relative to the fluorocarbon ion fluxes as the microwave power is increased or the chamber pressure is decreased. This relative increase in the F+ ion flux may be caused by the increased dissociation of the source gas. Changes in the ion flux composition seem to have little effect on the Si and SiO2 etch rates. It was also observed that the F+ ion flux increases as the percentage of hydrogen in a CHF3/H2 plasma is increased while the neutral fluorine optical emission intensity decreases for the same conditions. The data suggest that for these conditions dissociative ionization reactions involving fluorine containing molecules make a significant contribution to the production of F+, in addition to the ionization of neutral fluorine.