A method for forming a semiconductor device structure is provided. The method includes forming a first layer over a substrate. The method includes forming a stop layer over the first layer. The method includes forming a second layer over the stop layer. The second layer is in direct contact with the stop layer. The method includes partially removing the second layer. The method includes performing an etching process to partially remove the stop layer and an upper portion of the first layer, wherein protrusion structures are formed over a lower portion of the first layer after the etching process, and the protrusion structures include the stop layer and the upper portion of the first layer remaining after the etching process. The method includes removing the protrusion structures.