A new 2D molecular imprinting technique based on nanotemplating and soft-lithography techniques is reported. This technique allows the creation of target-specific synthetic recognition sites on different substrates using a uniquely oriented and immobilized template and the attachment of a molecularly imprinted polymer on a substrate. The molecularly imprinted polymer was characterized by AFM, fluorescence microscopy, and ATR-FTIR. We evaluated the rebinding ability of the sites with theophylline (the target molecule). The selectivity of the molecularly imprinted polymer was determined for the theophylline-caffeine couple. The molecularly imprinted polymer exhibited selectivity for theophylline, as revealed by competitive rebinding experiments. Fluorescence microscopy experiments provided complementary proof of the selectivity of the molecularly imprinted polymer surfaces toward theophylline. These selective molecularly imprinted polymers have the potential for chemical sensor applications. Because of its 2D nature, this novel chemical sensor technology can be integrated with many existing high-sensitivity multichannel detection technologies.