Layer-by-layer assembled polyelectrolyte multilayer films of poly(acrylic acid) (PAA)/poly(allylamine hydrochloride) (PAH) have been successfully patterned by room-temperature imprinting using a Norland Optical Adhesives (NOA 63) polymer mold. The proper amount of water in the PAA/PAH multilayer film can decrease the viscosity of the film and facilitate the imprinting. Many factors, such as imprinting pressure, length of imprinting time, and the structure and size of the patterns in the polymer mold, can produce an influence on the final imprinted pattern structures on multilayer films. A high imprinting pressure of 100 bar and elongated imprinting time of several hours is needed to achieve a patterned PAA/PAH multilayer film with a feature size of several tens of micrometers. With a twice imprinting, grid structures can be successfully produced when a NOA 63 mold having line structures is used. Room-temperature imprinting by using polymer NOA 63 mold provides a facile way to fabricate layered polymeric films with various kinds of pattern structures.