Disclosed is a method and apparatus for fabricating a patterned thin film layer within a flat panel display that employs a soft mold and heat treatment in place of a photolithographic process. The disclosed method may reduce process time as well as substantially minimize pattern deformities. A method of fabricating a thin film, a method and apparatus of fabricating a flat panel display according to an embodiment of the present invention includes the steps of forming a thin film on a substrate; coating an etch-resist solution including solvent over a substrate where the thin film has been formed; aligning a soft mold on the substrate provided with the etch-resist solution; forming a patterned etch-resist layer on the thin film by forming the etch-resist solution through a first heat treatment below the vaporization temperature of the solvent while pressure is applied to the soft mold on the etch-resist solvent; separating the soft mold from the patterned etch-resist layer; solidifying the patterned etch-resist layer through a second heat treatment; and etching the thin film by using the patterned etch-resist layer as a mask.