For photonic devices, extending beyond the planar regime to the third dimension can allow a higher degree of integration and novel functionalities for applications such as photonic crystals and integrated optical circuits. Although conventional photolithography can achieve both high quality and structural control, it is still costly and slow for three-dimensional (3D) fabrication. Moreover, as diverse functional polymers emerge, there is potential to develop new techniques for quick and economical fabrication of 3D structures. We present a 3D microfabrication technique based on the soft lithographic technique, called two-polymer microtransfer molding (2P-μTM) to accomplish low cost, high structural fidelity and tailorable 3D microfabrication for polymers. Using 2P-μTM, highly layered polymeric microstructures are achievable by stacking planar structures layer by layer. For increased processing control, the surface chemistry of the polymers is characterized as a function of changing ultraviolet dosage to optimize yield in layer transfer. We discuss the application of the 2P-μTM to build polymer templates for woodpile photonic crystals, and demonstrate methods for converting the polymer templates to dielectric and metallic photonic crystal structures. Finally, we will show that 2P-μTM is promising for fabricating 3D polymeric optical waveguides.