Various methods of fabricating substrate trenches and isolation structures therein are disclosed. In one aspect, a method of fabricating a trench in a substrate is provided. An oxide/nitride stack is formed on the substrate. An opening with opposing sidewalls is plasma etched in the silicon nitride film until a first portion of the oxide film is exposed while second and third portions of the oxide film positioned on opposite sides of the first portion remain covered by first and second portions of the silicon nitride film that project inwardly from the opposing sidewalls. The oxide film is etched for a selected time period in order to expose a portion of the substrate and to define first and second oxide/nitride ledges that project inwardly from the opposing sidewalls. The substrate is etched to form the trench with the first and second oxide/nitride ledges protecting underlying portions of the substrate.