In this paper, we present a novel rapid-prototyping process for out-of-cleanroom microfabrication of three-dimensional multilayer microfluidic structures with a 10 microm resolution, referred to as the Direct Projection on Dry-film Photoresist (DP(2)). A commercially available digital projector is customized to function as a direct mask generation and photo exposure system, while easy-processing photosensitive dry films are used as the microfluidic constructs. Multilayer alignments among maskless-patterned layers are reliably achieved by using a Software Alignment technique with less than 10 microm precision, which eliminates the use of mechanical travelling stage. The bonding between different layers of dry film, simply enabled by a plasma-assisted thermal lamination, offers an easy implementation for suspended multilayer microstructures. Development of a complex microfluidic chip from computer layout can thus be accomplished within an hour in a regular chemical or biological lab environment using this approach.