The present disclosure provides systems and methods for processing channel structures of substrates that include positioning the substrate in a first processing chamber having a first processing volume being in fluid communication with a plasma source. The substrate can include a channel structure with high aspect ratio features having aspect ratios greater than about 20:1. The method can also include forming an oxide cap layer over a silicon-containing layer of the channel structure and exposing the oxide cap layer to a hydrogen-or-deuterium radical to nucleate the silicon-containing layer of the channel structures of the substrate. Forming the oxide cap layer and exposing the channel structure with the hydrogen radical occurs in the first processing chamber to form a nucleated substrate. The method can also include positioning the nucleated substrate in a second processing chamber with a second processing volume and heating the nucleated substrate in the second processing chamber.