Methods of fabricating an isolation structure on a substrate are provided. In one aspect, a method of fabricating an isolation structure on a substrate is provided that includes forming a first insulating layer on the substrate wherein the first insulating layer has a first sidewall. A trench is formed in the substrate that has a second sidewall. A second insulating layer is formed in the trench. The second insulating layer displaces the second sidewall laterally. The first insulating layer is densified by heating to liberate gas therefrom and thereby move the first sidewall into substantial vertical alignment with the second sidewall. The risk of substrate attack due to trench isolation structure pullback is reduced. Trench edges are covered by thick isolation material.