Traditional optical fibers have been developed to achieve novel characteristics for both macro- and micro-applications. Inorganic optical waveguides using two-dimensional photonic crystals and silicon-on-insulator technology are examples of recent trends for macro- and micro-scale optical applications, respectively. As bio-photonics devices operate mostly with visible light, visible-transparent materials such as metal oxides and polymers are preferred as the guiding medium. Although polymers have tremendous potential because of their enormous variation in optical, chemical and mechanical properties, their application for optical waveguides is limited by conventional lithography. We present a non-optical lithographic technique, called two-polymer microtransfer molding, to fabricate polymer nano-waveguides, on-chip light sources and couplers. Micro-sources using quantum dots emitting red light (625nm) are successfully embedded in a waveguides array as the on-chip light sources. Fabrication of a grating coupler is also attempted for various external light sources including lasers and white light. We have quantified propagation losses of the waveguides using CCD photometry. The guiding loss is approximately 1.7dB/mm. We also demonstrated that the surface roughness of the fabricated waveguides can be reduced by chemical etching. We demonstrate that low cost, high yield, high fidelity, and tailorable fabrication of bio-photonic devices are achievable by the combination of the presented techniques.