A “drop-stamp method” has been developed for the design and fabrication of molecular interfaces. The amphiphilic protein HFBII, isolated from filamentous fungi, was employed as a genetically taggable molecular carrier for the formation of a structrally ordered layer of functional protein molecules on a solid surface. In this study, the interfacial behavior of maltose-binding protein tagged with HFBII (MBP-HFBII fusion protein) at both the air/water and water/solid interfaces was investigated. A rigid molecular layer of MBP-HFBII fusion protein was successfully formed through the drop-stamp procedure by employing an intermixed system, in which HFBII molecules are intermingled as nanospacers to prevent the intermolecular steric hindrance of the fusion protein. The results show that the drop-stamp method can be utilized in the high-throughput fabrication of structurally ordered molecular interfaces.