Anneal in reduced pressure hydrogen ambient is known to induce morphological changes in silicon microstructures via markedly increased surface self-diffusivity on exposed silicon surfaces. Here, we investigate the capillary instability of silicon nanostructures under hydrogen anneal. We demonstrate that a surface diffusion mask can significantly improve stability by isolating vulnerable segments from large mass reservoirs. In addition, we find that Plateau-Rayleigh instability shows strong crystallographic dependence, which is explained by the surface energy anisotropy of silicon. We observe that nanowires are the least stable when their axial orientation corresponds to 100 and are increasingly stable for 111, 112, and 110. © 2012 American Institute of Physics.