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A fast, effective process using hydrogen annealing is introduced to perform profile transformation on silicon-on-insulator (SOI) and to reduce sidewall roughness on silicon surfaces. By controlling the dimensions of as-etched structures, microspheres with 1 μm radii, submicron wires with 0.5 μm radii, and a microdisk toroid with 0.2 μm toroidal radius have been successfully demonstrated on SOI substrates. Utilizing this technique, we also observe the root-mean-square (rms) sidewall roughness dramatically reduced from 20 to 0.26 nm. A theoretical model is presented to analyze the profile transformation, and experimental results show this process can be engineered by several parameters including temperature, pressure, and time.