A two-step hydrogen anneal process has been developed for use in fabricating semiconductor nanowires for use in non-planar semiconductor devices. In the first part of the two-step hydrogen anneal process, which occurs prior to suspending a semiconductor nanowire, the initial roughness of at least the sidewalls of the semiconductor nanowire is reduced, while having at least the bottommost surface of the nanowire pinned to an uppermost surface of a substrate. After performing the first hydrogen anneal, the semiconductor nanowire is suspended and then a second hydrogen anneal is performed which further reduces the roughness of all exposed surfaces of the semiconductor nanowire and reshapes the semiconductor nanowire. By breaking the anneal into two steps, smaller semiconductor nanowires at a tight pitch survive the process and yield.