This paper investigates the end facet roughness of multimode polymer channel waveguides fabricated on FR4 printed circuit boards, PCBs, when cut at right angles to their optical axis by milling routers for optical butt-coupling connectors and compares it with that resulting from dicing saws and polishing and proposes a novel end facet treatment. RMS surface roughness of waveguide end facets, measured by AFMs, are compared for a range of rotation speeds and translation speeds of a milling router. It was found that one-flute routers gave significantly less rough surfaces than two or three-flute routers. The best results were achieved for a one-flute router when the milling bit was inserted from the PCB side of the board with a rotation speed of 15,000 rpm and a translation speed of 0.25 m/min which minimized the waveguide core end facet RMS roughness to 183 ± 13 nm and gave input optical coupling loss of 1.7 dB ± 0.5 B and output optical coupling loss of 2.0 dB ± 0.7 dB. The lowest RMS roughness was obtained at chip loads of 16 μm/revolution. High rotation speeds should be avoided as smearing of the end facet occurs possibly due to polymer heating and softening. For the first time to our knowledge, channel waveguide optical insertion loss is shown to be linearly proportional to the ratio of the waveguide core end facet RMS roughness to its autocorrelation length. A new fabrication technique for cut waveguide end facet treatment is proposed and demonstrated which reduces the insertion loss by 2.60 dB ± 1.3 dB which is more than that achieved by the closest available index matching fluid which gave 2.23 dB ± 1.2 dB. The new fabrication method gives a more robust end facet for use in commercial products.