A method of forming of a semiconductor structure has isolation structures. A substrate having a first region and a second region is provided. The first region and the second region are implanted with neutral dopants to form a first etching stop feature and a second stop feature in the first region and the second region, respectively. The first etching stop feature has a depth D1 and the second etching stop feature has a depth D2. D1 is less than D2. The substrate in the first region and the second region are etched to form a first trench and a second trench respectively. The first trench and the second trench land on the first etching stop feature and the second etching stop feature, respectively.