A method for forming a semiconductor device structure is provided. The method includes forming a first layer over a substrate. The first layer is made of a semiconductor material. 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 removing the second layer. The method includes performing an etching process to remove the stop layer and an upper portion of the first layer. The method includes performing a first planarization process over the first layer.