The mild conditions and specificity of biological catalysts are attractive incentives for their use in the formation of surfaces with well-defined chemical functionality. Herein, we describe the synthesis, characterization, and enzymatic modification of a functionalized polymeric bilayer assembly. The assembly is composed of a self-assembled monolayer of octadecylsilane and a Langmuir-Blodgett monolayer of polydiacetylene functionalized with the dipeptide phenylalanine-alanine (Phe-Ala). We demonstrate via X-ray photoelectron spectroscopy surface analysis that the surface-bound Phe-Ala dipeptide is a substrate for specific cleavage by the enzyme subtilisin BPN’. In-situ surface transformations via enzymatic synthesis or cleavage offer an alternative to chemical treatments of organic thin films.