Methods of passivating at least one facet of a multilayer waveguide structure can include: cleaning, in a first chamber of a multi-chamber ultra-high vacuum (UHV) system, a first facet of the multilayer waveguide structure; transferring the cleaned multilayer waveguide structure from the first chamber to a second chamber of the multi-chamber UHV system; forming, in the second chamber, a first single crystalline passivation layer on the first facet; transferring the multilayer waveguide structure from the second chamber to a third chamber of the multi-chamber UHV system; and forming, in the third chamber, a first dielectric coating on the first single crystalline passivation layer, in which the methods are performed in an UHV environment of the multi-chamber UHV system without removing the multilayer waveguide structure from the UHV environment.