A method of forming a semiconductor structure includes implanting neutral dopants in a first region of a substrate to form a first etching stop feature, the first etching stop feature having a depth D1. The method further includes implanting neutral dopants in a second region of the substrate to form a second etching stop feature, wherein the second etching stop feature has a depth D2, and D1 is different from D2. The method further includes etching the substrate to form a first trench and a second trench, wherein the first trench and the second trench expose the first etching stop feature and the second etching stop feature, respectively. The method further includes filling the first trench and the second trench with a dielectric material.