Chalcogenides are a promising platform for infrared nonlinear optics but are susceptible to structural changes during fabrication that affect their linear and nonlinear optical properties. We analyze the structure and optical properties of thermally evaporated and annealed chalcogenide films. Thermally evaporated Ge 28 Sb 12 Se 60 has an increased selenium content, bandgap, and concentration of heteropolar bonds. The concentration of heteropolar bonds can be reduced by annealing above the glass transition temperature, resulting in improved optical nonlinearity. We demonstrate a 4-fold enhancement of third-order nonlinearity in Ge 28 Sb 12 Se 60 chalcogenide waveguides by thermal annealing and a decrease in propagation loss from 2.5 dB/cm to 1 dB/cm as an added benefit.