We demonstrate a new approach to the study and application of microwave-induced chemical reactions, using a purpose-designed molecular film as a discrete ultrathin antenna that can utilize absorbed electromagnetic energy to directly drive a specific chemical transformation. Exposure of such a bilayer "antenna" self-assembled on silicon to common microwave radiation in a domestic oven is shown to reproducibly generate a depleted top monolayer structure with molecular-size vacancies that can incorporate and control the further surface manipulation of various gap-fitting guest species. The nonthermal nature of this process is unequivocally demonstrated, as the irradiated bilayer cannot store heat, while conventional heating causes its irreversible structural deterioration, before an equivalent thermally activated transformation could occur. These findings shed new light on the much disputed issue of nonthermal microwave effects, suggesting, beyond obvious implications for basic research in this area, that microwave radiation could be rationally utilized to achieve specific (nondestructive) transformations in properly designed supramolecular systems and could be utilized particularly as an attractive new synthetic tool in molecular surface engineering.