We present a method to etch vertical and smooth silicon sidewalls. The so-called modified Bosch process combines a passivation step, a breakthrough step, and an anisotropic etch step within one repeatable loop. Thanks to the sidewall protection from the passivation step and the anisotropic nature of the etch step, this method can etch smoother silicon sidewalls than either a typical Bosch process or a continuous anisotropic etch process. The silicon sidewall of a 4-μm-deep waveguide structure etched by this method has a root mean square roughness below 10 nm and a peak-to-valley (P-V) roughness below 60 nm. Comparisons between silicon waveguides etched by this process and by another deep reactive-ion etching process showed remarkable improvement in propagation loss at the wavelength of 1550 nm.