The microstructure and thermal stability of multilayer thin films of rodlike polyglutamate copolymers having flexible aliphatic side chains have been studied with X-ray and neutron reflectometry. The complementary sensitivity of X-rays and neutrons and the use of four different sequences of protonated and deuterated molecules provides an enhanced level of structural discrimination. Within bilayers formed upon deposition, the backbones are located preferentially near the center, with backbones from the two layers overlapping strongly. The side chains of molecules in adjacent layers belonging to different bilayers interdigitate substantially, and interdigitation between layers within a bilayer is seen as well. Upon annealing at 70 or 84 degrees C, the backbone positions within each bilayer relax. However, there is no ascertainable interlayer interdiffusion and the nature of the side chain interdigitation does not change. No evidence is found for the formation, with annealing, of a three-dimensional ordered structure.