A STI (shallow trench isolation) structure is formed with a liner layer that is converted from an initial material to a subsequent material. For example, the liner layer is initially comprised of nitride during wet etch-back of a dielectric fill material comprised of oxide to protect an oxide layer on a semiconductor substrate. Thereafter, an exposed portion of the liner layer is converted into the subsequent material of oxide to protect the dielectric fill material within the STI opening during etching away of masking layers to prevent formation of dents in the STI structure.