Electro-optical printed circuit board technology (EOCB) based on integrated planar polymer optical waveguides has been the subject of research and development for many years to provide a cost viable, fully integrated system embedded optical interconnect solution, however a number of constraints of this technology have yet to be overcome. Optical coupling loss at the input and output of the waveguides is one of the major issues and waveguide end facet roughness is one of the main sources of the coupling loss which is investigated in this paper. The results of a comprehensive investigation of the end facet roughness of multimode polymer waveguides, fabricated on FR4 printed circuit boards, PCBs, and its effect of optical loss are presented theoretically and experimentally. The waveguide end facet roughness was measured using an atomic force microscope, AFM, when the waveguides were cut using a milling router with various numbers of cutting edges called flutes. The optimized cutting parameters are derived and the optical coupling loss, between the laser source and the waveguide, due to the different roughness magnitudes is measured by experiment for the first time. To improve the surface quality and decrease the waveguide optical loss, a new fabrication technique for reducing the end facet roughness after cutting is proposed and demonstrated. The insertion loss was reduced by 2.60 dB ± 1.3 dB which is more than that achieved by other conventional methods such as index matching fluid.