A method of fabricating a shallow trench isolation includes formation of a polishing stop layer. The polishing stop layer is formed in a fill material by performing ion implantation to implant atoms in the fill material. The depth of the polishing stop layer can be controlled by the energy of the implanted atoms. The polishing stop layer prevents the fill material from being dished by chemical-mechanical polishing. The polishing stop layer also prevents scratches from forming in the surface of the fill material, which is used to form isolation regions.