The mesoscale surface morphology and molecular scale ordering of Langmuir-Blodgett (LB) bilayers of a polyglutamate statistical copolymer substituted with octadecyl side chains on 30 % of its repeat units has been investigated using atomic force microscopy to elucidate those structural features important for their optical properties. Although a vast majority of all surfaces observed are extremely smooth on the mesoscale, a variety of interesting morphologies are observed on the remaining surface. Bilayers deposited directly on silicon substrates are seen to differ substantially from those deposited on a supporting LB multilayer of either polyglutamate (PG) or cadmium arachidate. Also the ability to capture molecular scale images of the surface and the stability of the surface to scan-induced damage depend on the supporting material. Use of a higher force during scanning in a selected sample area produces a local scraping of the PG film. By this method, square holes with 1.6-4.0-nm depths and sizes of 30-500 nm can be produced at selected sites in the films.