Biological membranes play essential roles in living organism. However, their functions are not yet well understood owing to the complex and dynamic nature of the membrane. We are developing a synthetic model system of the biological membranes on solid substrate for basic biophysical studies as well as biomedical applications. An important structural feature of the biological membrane is the combination of two-dimensional (2D) and three-dimensional (3D) architectures that create compartments in the cell and cell-cell junctions. We have been developing a micro-patterned membrane of polymerized and natural lipid bilayers that mimics the 2D structure of the biological membrane. For mimicking the 3D compartments, we have developed a nanometric gap structure on the patterned membrane by attaching the polymeric bilayer with a silicone elastomer (PDMS) using an adhesion layer having a defined thickness (nanogap-junction). These integrated model system should provide novel opportunities to study the membrane functions and exploit them in biomedical applications.