Self-written polymer waveguide is a polymer interconnection structure often integrated with optical fibers. The structure is fabricated by photopolymerization, through which a photon beam initiates a polymerization reaction to change liquid monomer into a solid polymer. During light-matter interaction photoinitiator molecules are excited to the singlet and then to the third state to form free radicals by attaching to the adjacent monomer molecules. The free radicals in turn form polymer chains and cross-linked structures. Photo-induced polymerization leads to a raised refractive index of the monomer and forms an optical waveguide. The change is permanent to allow the process of self-focusing and self-trapping of the propagation light beam and hence guide it to the aligned optical fiber. In this article, light matter interaction during polymer waveguide fabrication and post polymerization has been investigated. A photopolymer system of acrylate-based monomer, co-initiator amine and photo initiator is used to study the absorption of the monomer mixture at the spectral range of 450–550 nm. Then photobleaching was investigated after waveguide fabrication. The optical transmission efficiency of the polymer bridge increases as absorption ceases within the polymer structure such that optical loss reduces from 1.1 dB to about 0.65 dB.