The authors propose a novel post-focused- ion -beam (FIB) treatment method to improve the optical properties of photonic devices fabricated by the Ga+ FIB technique on the silicon substrate with low temperature liquid annealing process. A conventional micrometric ridge waveguide is first fabricated and then annealed to roughly detect the improvement of its optical properties. Then a nanometric 12-fold photonic quasicrystal waveguide is designed to further study its topography variation as well as the subtle influence on its optical properties with different post-FIB treatments. By comparing the experimental results with the theoretical results that are made by means of the three-dimensional finite-difference time-domain method, the authors find that the proposed low temperature liquid annealing method can efficiently improve the optical properties of photonic devices by decreasing Ga+ contamination, removing redeposited Si-SiO2 composites, and restoring damaged silicon lattice structures caused by Ga+ bombardment in the FIB micromachining. (C) 2007 American Vacuum Society.