The optical data transfer is considered as the future of signal transfer due to its various advantages compared to conventional copper-based technologies. The Aerosol Jet Printing (AJP) technology offers the opportunity to print materials with high viscosities, such as liquid transparent polymer adhesives (epoxy resins), on almost any possible substrate material and even in third dimension. This paper introduces a new flexible and comparatively cost-effective way of generating polymer optical waveguides through AJP. Furthermore, the conditioning of the substrate material and the printing process of planar waveguides are presented. In the first step, two lines with hydrophobic behavior are applied on foil material (PMMA, PVC, PI) by using a flexographic printing machine. These silicone based patterns containing functional polymer form barriers for the core material due to their low surface energy after curing. In the second step, the core material (liquid polymer, varnish) is printed between the barrier lines. Because of the hydrophobic behavior of the lines, the contact angle between the substrate surface and the liquid core material is increased which yields to higher aspect ratio. The distance between the barrier lines is at least 100 μm, which defines the width of the waveguide. The minimum height of the core shall be 50 μm. After UV-curing of the core polymer, the cladding material is printed on the top. This is also applied by using the AJP technology. Various tests were performed to achieve the optimal surface properties for adequate adhesion and machine process parameters.