Self-organized ordered microstructure formation under the action of van der Waals forces is studied in thin (<100 nm) viscous bilayers through nonlinear simulations. For ultra-thin (<100 nm) films, intermolecular forces dominate over the other body forces, thus simulating microgravity conditions needed for fabrication of non-distorted ordered patterns. In particular, we concentrate upon a special type of bilayer in which only the lower layer is unstable and the upper layer is unconditionally stable to fabricate embedded microstructures. The patterns on the films are fabricated by employing either a topographically or chemically patterned solid substrate to control the spatial strength of the intermolecular force. The conditions are identified to fabricate a number of interesting interfacial morphologies such as: (a) embedded microchannels of herringbone shape, (b) encapsulated and embedded droplets of spatially varying shape, and (c) perforated membranes. Our study shows that this methodology can not only lead to ordered patterns, but is also capable of pattern replication because the patterns formed at the embedded liquid-liquid interface are also transferred to the free and stable liquid-air interface.