A hybrid μ-stereolithography system that combines conventional μ-stereolithography and aerosol jet printing techniques has been developed for the fabrication of polymer-based waveguide structures with high resolution on free-form surfaces. The aerosol jet printing system allows coating uniform polymer layers for a layer-by-layer process in μ-stereolithography. In the experiments Ormocer® is used as a polymer material for the waveguide cores. Pentaerythritol triacrylate (PETA) is used for the waveguide cladding. The obtained core parts with elliptical cross section show a smooth surface with 39 nm of average roughness (Ra) that fulfills the conditions for guiding light. Ormocer® and PETA have enough difference in refractive index for light propagation inside the waveguide. Guiding a laser beam with 532 nm wavelength has been demonstrated using a fabricated waveguide structure. The propagation of the laser beam was in multi-mode. The hybrid μ-stereolithography process can become a fabrication technique for polymer-based waveguides as a next generation of optical interconnects in photonic integrated circuits.