Embodiments of the disclosure provide an improved apparatus and methods for nitridation of stacks of materials. In one embodiment, a method for processing a substrate in a processing region of a process chamber is provided. The method includes generating and flowing plasma species from a remote plasma source to a delivery member having a longitudinal passageway, flowing plasma species from the longitudinal passageway to an inlet port formed in a sidewall of the process chamber, wherein the plasma species are flowed at an angle into the inlet port to promote collision of ions or reaction of ions with electrons or charged particles in the plasma species such that ions are substantially eliminated from the plasma species before entering the processing region of the process chamber, and selectively incorporating atomic radicals from the plasma species in silicon or polysilicon regions of the substrate.