Methods and apparatus for selective one-step nitridation of semiconductor substrates is provided. Nitrogen is selectively incorporated in silicon regions of a semiconductor substrate having silicon regions and silicon oxide regions by use of a selective nitridation process. Nitrogen containing radicals may be directed toward the substrate by forming a nitrogen containing plasma and filtering or removing ions from the plasma, or a thermal nitridation process using selective precursors may be performed. A remote plasma generator may be coupled to a processing chamber, optionally including one or more ion filters, showerheads, and radical distributors, or an in situ plasma may be generated and one or more ion filters or shields disposed in the chamber between the plasma generation zone and the substrate support.