The first section of this paper presents an overview of the examination and treatment of two seventeenth century stained glass panels. The panels were in good condition and showed a variety of techniques common in stained glass manufacture as well as some expertly executed replacement fills from previous restorations. The panels required treatment because of accumulated surface grime and corrosion products and because mending leads were obscuring important design elements. The second part of this paper discusses the structure of glass and the role of fluxes in the deterioration of glass. Scanning electron microscopy was used to determine the components of the glass and to clarify the windows in terms of their durability based on the types and amount of flux.