Proton beam writing (PBW) is a lithographic technique that utilizes MeV protons in a direct write mode to fabricate micro/nano features in suitable resist material (E.g PMMA, SU-8, silicon, Foturan). These micro/nano structures may be used in an electroplating step to yield robust metallic stamps/molds for the replication of the original and lends itself to the fabrication of micro/nano fluidic channels that are important components in devices such as biophotonic chips. Another feature of proton bombardment is its ability to induce an increase in refractive index along the ions path, in particular at the end of its range where there is substantial nuclear scattering. This allows PBW to directly write buried waveguides that can be accurately aligned with fluidic channels. Polydimethylsiloxane (PDMS) is an optically clear, biocompatible polymer that can be readily used with a mold (such as that created with PBW) and easily sealed so as to produce biophotonic chips containing micro/nano fluidic channels. This has lead us to favour PDMS as the base material for our work on the development of these biophotonic chips. The present work is concerned with the production of integrating channel waveguides in PDMS chips, so as to have a working device that may be used to detect fluorescently tagged biological samples. For this we have adopted two approaches, namely(1) directly embedding optical fibres in the polymer and (2) using PBW to directly write buried waveguides in the polymer.