A method of protecting alignment marks from damage in a planarization process includes providing a substrate including a surface, forming trenches in the substrate from the surface, forming a first dielectric layer on the substrate, forming a second dielectric layer on the first dielectric layer, forming a patterned second dielectric layer by removing second dielectric over the trenches, resulting in openings defined by the trenches and the patterned second dielectric layer, forming a third dielectric layer on the patterned second dielectric layer, the third dielectric layer filling the openings, and planarizing the third dielectric layer by using the patterned second dielectric layer as a stop layer, resulting in residual third dielectric in the openings that includes a first portion in the substrate and a second portion above the surface of the substrate.