Implementations disclosed herein provide a method of reducing the topography at the alignment and overlay marks area during the writer pole photolithography process in order to reduce the wafer scale variation and reduce the writer pole photolithography process rework rate. In one implementation, an intermediate stage of a wafer for writer pole formation is generated by removing a part of at least one metallic writer pole layer on top of an intermediate stage writer pole wafer to form a recovery trench, depositing an optically transparent material on top of the wafer, wherein the thickness of the optically transparent material is higher than a target recovery trench topography, forming a photoresist pattern on top of the optically transparent material over the recovery trench, etching the optically transparent material, and removing the photoresist pattern and at least part of the remaining optically transparent material.