System and method for radical and thermal processing of substrates

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. The substrate includes a channel structure with high aspect ratio features having aspect ratios greater than about 20:1. The method includes forming a silicon-containing layer over the channel structure to a hydrogen-or-deuterium plasma in the first processing volume at a flow rate of about 10 sccm to about 5000 sccm. The substrate is maintained at a temperature of about 100° C. to about 1100° C. during the exposing, the exposing forming a nucleated substrate. Subsequent to the exposing a thermal anneal operation is performed on the substrate.