A method includes etching a semiconductor substrate to form trenches extending into the semiconductor substrate, and depositing a first dielectric layer into the trenches. The first dielectric layer fills lower portions of the trenches. A Ultra-Violet (UV) treatment is performed on the first dielectric layer in an oxygen-containing process gas. The method further includes depositing a second dielectric layer into the trenches. The second dielectric layer fills upper portions of the trenches. A thermal treatment is performed on the second dielectric layer in an additional oxygen-containing process gas. After the thermal treatment, an anneal is performed on the first dielectric layer and the second dielectric layer.