We present micro polymer optical waveguide elements fabricated using femtosecond laser and two-photon absorption (TPA) process. The POWs are constructed by tightly focusing a laser beam in SU-8 based resists transparent to the laser wavelength for single-photon absorption. The TPA process enables the patterning of the resist in three dimensions at a resolution of 100-200 nm, which provides a high degree of freedom for POW designs. Using this technology, we provide a novel approach to fabricate Three dimensional Polymer Optical Waveguides (3D-POW) and coupling with single mode fibers in the visible wavelength regions. Our research is also focused on fabricating passive micro optical elements such as splitters, combiners and simple logical gates. For this reason we are aiming to achieve optimum coupling efficiency between the 3D-POW and fibers. The technology also facilitates 3D-POW fabrication independent of the substrate material. We present these fabrication techniques and designs, along with supporting numerical simulations and its transmission properties. With a length of 270 μm and polymer core diameter of 9 μm with air cladding, the waveguides possess a total loss of 12 dB. This value also includes the external in and out mode coupling and in continuously being improved upon by design optimization and simulations. We verify the overall feasibility of the design and coupling mechanisms that can be exploited to execute waveguide based optical functions such as filtering and logical operations.