We report the fabrication of micro/nanoscale pits with facile shape, orientation, and size controls on an Si surface via an Au-nanoparticles-assisted vapor transport method. The pit dimensions can be continuously tuned from 70 nm to several mum, and the shapes of triangles, squares, and wire/hexagons are prepared on Si (111), (100), and (110) substrates, respectively. This reliable shape control hinges on the anisotropic diffusivity of Co in Si and the sublimation of cobalt silicide nanoislands. The experimental conditions, in particular the substrate orientation and the growth temperature, dictate the pit morphology. On the basis of this understanding of the mechanism and the morphological evolution of the pits, we manage to estimate the diffusion coefficients of Co in bulk Si along the 100 and 111 directions, that is D(100) and D(111). These diffusion coefficients show strong temperature dependence, for example, D(100) is ca. 3 times larger than D(111) at 860 degrees C, while they approach almost the same value at 1000 degrees C. This simple bottom-up route may help to develop new technologies for Si-based nanofabrication and to find potential applications in constructing nanodevices.