A method for forming alignment marks are disclosed for performing photoalignment after chemical-mechanical polishing (CMP). A trench is first formed in a silicon substrate and then alignment marks are formed at the bottom of the trench. The aspect ratio of the trench is selected to be so low that the dishing of the CMP pad can be prevented from reaching into the trench to damage the alignment marks therein. A trench structure is also provided whereby the alignment marks can be protected from the abrasive action of the CMP. Steps subsequent to the CMP can therefore proceed unimpeded with the presence of undamaged alignment marks.