Fiber-optic comb filters using a side-polished fiber coupler are proposed as multi-channel isolation filters on wavelength division multiplexing systems. We have demonstrated that the coupling efficiency between two waveguides is improved by the intermediate coupling layer in spite of the decrease of the optical power transfer between two waveguides due to the high-order modes of the overlay waveguide coupled with the side-polished single-mode fiber. When LiNbO$_3$with a 200-${mu}{ extrm}{m}$-thickness was applied as a planar-overlay-waveguide, the comb filtering characteristics with a 4 nm-channel-spacing were achieved and the maximum power coupling occurred at the 1-${mu}{ extrm}{m}$-thickness and the refractive index in range 1.52 to 1.53 of an intermediate coupling layer. If the intermediate coupling layer is optimized, an extinction ratio with more than 20 dB can be obtained. These experimental results are in good agreement with the BPM simulation.