Reproducible carbon/molecule/Cu molecular junctions are made with high yield using diazonium reduction of aromatic molecules on carbon with direct evaporation of Cu as a top contact. This report investigates the stability of these devices in response to fabrication steps. Raman spectroscopy through a transparent support shows that direct deposition of Au or Cu causes little change in molecular layer structure, while Ti and Pt deposition cause significant damage to the molecules. AFM, Raman, and XPS examination of Au, Cu, and Ti devices after removal of deposited metal confirm that Cu and Au have minimal effects on molecular structure. However, the molecular layer is rougher after Au deposition, probably due to partial penetration of Au atoms into the molecular layer. Completed carbon/molecule/Cu devices can be heated to 250 degrees C without significant changes in electronic behaviour while nitroazobenzene molecular layers on carbon were unaffected by photolithography or by 5 min at 400 degrees C in vacuum. Completed devices could be sealed with parylene-N, stabilizing them to aqueous etching solution. The stability of carbon/molecule/Cu junctions is due, in part, to the strong carbon-carbon bonding and aggressive nature of diazonium surface modification. The results significantly expand the range of processing variables compatible with molecular electronic junctions.