The optimum processing parameters for the fabrication of low‐loss waveguides in fused silica by ion implantation and annealing have been determined through a comparison of implantation‐induced physical and optical properties. The step height at an implanted/unimplanted boundary resulting from Si implantation was measured as a function of the ion dose (2×1012–6×1016/cm2) and energy (1–9 MeV) and the postimplantation annealing temperature (200–900 °C) and time (0.1–150 min). For a given ion energy (5 MeV), the step height increased for doses <∼1015/cm2and thereafter, saturated. For a given ion dose (2×1015/cm2), a near‐linear trend was evident for step height as a function of ion energy. Isochronal and isothermal annealing both resulted in a nonlinear reduction in step height, typical of a thermally induced process. In contrast to the continual reduction in step height observed during isochronal annealing, the loss coefficient exhibited a distinct minimum of ∼0.15 dB/cm at an intermediate temperature of 500 °C. This feature was consistent with the removal of a specific defect or color center. ©1996 American Institute of Physics.