Ion implantation of semiconductors is a very attractive technique for forming the guided wave components needed in integrated optical circuits. Implanted protons produce lattice defects which act as electron traps, thereby lowering the free carrier concentration and the subsequent negative plasma contribution to the index of refraction, producing waveguiding. Careful control of implant parameters, along with post-implant thermal annealing, allow optimization of defect annealing and diffusion sufficient to reduce the waveguiding loss and to provide the precise desired waveguided mode structure. Due to the statistical nature of the implantation, precise device practicality is achieved, along with planar waveguides exhibiting losses at 1.15 μm less than 2 cm-1. Characterization of the effects of thermal processing on the optical and electronic properties of proton implanted n-type GaAs is reported. The thermal processing includes variations in the substrate temperature during implantation and post-implantation annealing. Capacitance-voltage and infrared reflectivity measurements provide a measurement of the degree, depth, and uniformity of compensation, while free carrier absorption loss in the substrate mode tails and optical guided mode profiles are obtained using a scanning galvanometer mirror and a detector slit. A revised theoretical model of the compensation process based upon the classical Drude model is presented along with a variety of unique loss and mode profile determinations correlated with implant fluence and temperature processing.