A method includes performing an anisotropic etching on a semiconductor substrate to form a trench. The trench has vertical sidewalls and a rounded bottom connected to the vertical sidewalls. A damage removal step is performed to remove a surface layer of the semiconductor substrate, with the surface layer exposed to the trench. The rounded bottom of the trench is etched to form a slant straight bottom surface. The trench is filled to form a trench isolation region in the trench.