A polymer optical waveguide interleaver with selectable channel spacing and adjustable flat top based on a three-dimensional structure is reported. This interleaver is made of two waveguides laid in two different but parallel layers. These two waveguides cross-over each other three times, with an electrode heater deposited on top of each crossing point to adjust the coupling ratio between the guides. This 3D structure has many advantages over the corresponding 2D counterpart such as the ease of fabrication and the adjustment of coupling ratio between the two waveguides. The channel spacing can be selected to be either 1.6 nm, 0.8 nm or 0.53 nm simply by changing the power supplied to each heater; also at the 1.6 nm channel spacing it is possible to create a flat-top spectral response (0.6 dB ripple over 0.5 nm), again by tuning the coupling ratios using the electrical heaters.