Analysis of chemical downstream etch processes investigates ion and radical generation in a plasma source, the transport of species through a transport tube to the process chamber, and resulting etch behavior in the downstream reactor. Downstream etching of silicon dioxide or polysilicon material on a wafer results from chemical etching by F atoms, while ion flux to the wafer must be minimal to avoid ion-induced device damage. In the plasma source, results for NF3 chemistry show that F is the dominant neutral species, while NF2+ and F- are the dominant ions. Comparison of species concentrations in a plasma source with mass spectrometry data available in the literature shows good quantitative agreement. Inclusion of a quartz-etch mechanism within the plasma source reproduces observed erosion rates of quartz applicators used in these systems. Ions persist a small distance beyond electrons in the transport tube region due to negative ion content, but the ion density is reduced to very low levels after traversing the length of the transport tube. The addition of oxygen generally reduces the F-atom concentration downstream and changes the ion composition. Analysis of the reacting flow in the downstream chamber shows the role of species diffusion in determining the etch uniformity and species concentration profiles. Predicted downstream etch rates agree well with measured data over a wide range of process conditions.