We introduce a simple intermembrane junction system in which to explore pattern and structure formation by membrane-bound proteins. The junction consists of a planar lipid bilayer to which one species of protein (an IgG antibody) is bound, forming a 2D, compressible fluid. Upon the adhesion of a second lipid bilayer, the formerly uniformly distributed proteins rapidly reorganize into patterns of dense and sparse zones. Using a combination of complementary imaging techniques (fluorescence microscopy, fluorescence interference contrast microscopy, and fluorescence resonance energy transfer), we reconstruct the 3D structure of these intermembrane patterns with nanometer-scale topographic resolution, revealing the orientation of the proteins. The patterns form as the rapid bilayer-bilayer adhesion, often radiating outward from an initial, circular contact site, pushes aside the antibodies, sweeping them into areas of high density and clearing low-density regions. Coarsening of these local features is energetically costly and therefore kinetically trapped; the patterns do not change over tens of minutes. These studies demonstrate that membrane mechanical forces alone, i.e., in the absence of specific biochemical interactions, can drive m-scale organization of membrane proteins.