The mechanism of self-assembly by short-chain peptides (oligopeptides) – the process by which their molecules spontaneously form an ordered structure – has received much attention recently. Self-assembling phenylalanine oligopeptides have been of particular interest due to their potential as an effective aid in the design of new functional materials. This paper considers the results of an SPM study on the ability of L-alanyl-L-phenylalanine to self-assemble into a thin film under the action of methanol vapor. The micro- and nanostructures that develop on the surface of amorphous films of this dipeptide were characterized. A method for monitoring the state of the surface of dipeptide films using atomic force spectroscopy was proposed. The results obtained contribute to the development of approaches for the controlled self-assembly of oligopeptides used to produce new biocompatible materials and environmentally friendly micro- and nanodevices that would help solve various problems in the medical, environmental, and energy fields.