Methods for performing a pre-clean process to remove an oxide in semiconductor devices and semiconductor devices formed by the same are disclosed. In an embodiment, a method includes forming a shallow trench isolation region over a semiconductor substrate; forming a gate stack over the shallow trench isolation region; etching the shallow trench isolation region adjacent the gate stack using an anisotropic etching process; and after etching the shallow trench isolation region with the anisotropic etching process, etching the shallow trench isolation region with an isotropic etching process, process gases for the isotropic etching process including hydrogen fluoride (HF) and ammonia (NH3).