A method for removing nuclei formed during a selective epitaxial growth process includes epitaxially growing a first group of one or more semiconductor structures over a substrate with one or more mask layers. A second group of a plurality of semiconductor structures is formed on the one or more mask layers. The method also includes forming one or more protective layers over the first group of one or more semiconductor structures. At least a subset of the second group of the plurality of semiconductor structures is exposed from the one or more protective layers. The method further includes, subsequent to forming the one or more protective layers over the first group of one or more semiconductor structures, etching at least the subset of the second group of the plurality of semiconductor structures.