We demonstrate control of the structure and morphology of polypeptide/surfactant films at the air/water interface as a function of the maximum compression ratio of the surface area, exploiting a recently developed film formation mechanism that requires minimal quantities of materials involving the dissociation of aggregates. The systems studied are poly(L-lysine) (PLL) or poly(L-arginine) (PLA) with sodium dodecyl sulfate (SDS), chosen because the surfactant (i) interacts more strongly with the latter polypeptide due to the formation of hydrogen bonds between the guanidinium group and its oxygen atoms, and (ii) induces bulk β-sheet and α-helix conformations of the respective polypeptides. The working hypothesis is that such different interactions may be used to tune the film properties when compressed to form extended structures (ESs). Neutron reflectometry reveals that application of a high compression ratio (4.5 : 1) results in the nanoscale self-assembly of ESs containing up to two PLL-wrapped SDS bilayers. Brewster angle microscopy provides images of the PLL/SDS ESs as discrete regions on the micrometre scale while additional linear regions of PLA/SDS ESs mark macroscopic film folding. Ellipsometry demonstrates high stability of the different ESs formed. The collapse of PLL/SDS films upon compression to a very high ratio (10 : 1) is irreversible due to the formation of solid domains that remain embedded in the film upon expansion while that of PLA/SDS films is reversible. These findings demonstrate that differences in the side group of a polypeptide can have a major influence on controlling the film properties, marking a key step in the development of this new film formation mechanism for the design of biocompatible and/or biodegradable films with tailored properties for applications in tissue engineering, biosensors and antimicrobial coatings.