Methods for etching silicon using hydrogen radicals in a hot wire chemical vapor deposition process are provided herein. In some embodiments, a method of processing a substrate having a crystalline silicon layer atop the substrate and a patterned masking layer atop the crystalline silicon layer exposing portions of the crystalline silicon layer; the method may include (a) exposing the substrate to a plasma formed from an inert gas wherein ions from the plasma amorphize a first part of the exposed portions of the crystalline silicon layer; and (b) exposing the substrate to hydrogen radicals generated from a process gas comprising a hydrogen-containing gas in a hot wire chemical vapor deposition (HWCVD) process chamber to etch the amorphized first part of the exposed portion of the crystalline silicon layer.