A method of annealing a substrate comprising a trench containing a dielectric material, the method including annealing the substrate at a first temperature of about 200° C. to about 800° C. in a first atmosphere comprising an oxygen containing gas, and annealing the substrate at a second temperature of about 800° C. to about 1400° C. in a second atmosphere lacking oxygen. In addition, a method of annealing a substrate comprising a trench containing a dielectric material, the method including annealing the substrate at a first temperature of about 400° C. to about 800° C. in the presence of an oxygen containing gas, purging the oxygen containing gas away from the substrate, and raising the substrate to a second temperature from about 900° C. to about 1100° C. to further anneal the substrate in an atmosphere that lacks oxygen.