In this paper, we report a direct-write technique for three-dimensional control of waveguide fabrication in silicon. Here, a focused beam of 250 keV protons is used to selectively slow down the rate of porous silicon formation during subsequent anodization, producing a silicon core surrounded by porous silicon cladding. The etch rate is found to depend on the irradiated dose, increasing the size of the core from 2.5 microm to 3.5 microm in width, and from 1.5 microm to 2.6 microm in height by increasing the dose by an order of magnitude. This ability to accurately control the waveguide profile with the ion dose at high spatial resolution provides a means of producing three-dimensional silicon waveguide tapers. Propagation losses of 6.7 dB/cm for TE and 6.8 dB/cm for TM polarization were measured in linear waveguides at the wavelength of 1550 nm.