We present the fabrication and characterization of inter-layer single-mode light-guiding structures in a newly developed photo-structurable polymer via femtosecond laser writing. A host-guest polymer system utilizing external diffusion induces permanent and high refractive index modulation. Analyzing the complete curing and the impact of external diffusion on refractive index profile helps optimize the fabrication process. The fabrications of 4 × 2 array interconnect and 3-waveguide core fan-out device involve only a single layer, and need no stacking or alignment effort. The resulting pitch size and crosstalk between single-mode waveguides are 25 μm and −34 dB, respectively. Adding sensitizer into the photopolymer to increase its sensitivity in two-photon polymerization at a writing wavelength of 390 nm reduces the surface roughness of written structures by a factor of seven.