Methods for applying topographically compensated film in a semiconductor wafer fabrication process are disclosed. The processes include premapping a surface of a wafer so as to determine the local topography (e.g., z-height) of the wafer and then applying a variable depth of a film to the wafer, such that the variable depth is modulated based on the local topography of the wafer. The resultant topography of the applied film and wafer is substantially planar (e.g., within approximately 100 nm) across the wafer.