A detailed study of photo-inscribed optical waveguides in PMMA and polycarbonate using a mid-IR laser is presented. The wavelength of the laser is tuned near the absorption peaks of stretching C-H molecular bonds and the focused beam is scanned onto the surface of planar polymer samples. For the first time, we report the formation of optical waveguides in both polymers through resonant absorption of the laser beam. The optical properties of the waveguides were thoroughly assessed. An elliptic Gaussian mode is guided at the surface of both polymers. Insertion losses of 3.1 dB for a 30 mm long on-surface waveguide inscribed in PMMA were recorded. Such waveguides can interact with the external medium through evanescent coupling. As a proof of concept, the surface waveguides are used as highly sensitive refractometric sensors. An attenuation dynamical range of 35 dB was obtained for a liquid that matches the index of the PMMA substrate. Our results pave the way for large scale manufacturing of low cost biocompatible photonic devices.