Method and apparatus for controlling topographical variation on a milled cross-section of a structure

An improved method of controlling topographical variations when milling a cross-section of a structure, which can be used to reduce topographical variation on a cross-section of a write-head in order to improve the accuracy of metrology applications. Topographical variation is reduced by using a protective layer that comprises a material having mill rates at higher incidence angles that closely approximate the mill rate of the structure at those higher incidence angles. (702) Topographical variation can be intentionally introduced by using a protective layer that comprises a material having mill rates at higher incidence angles that do not closely approximate the mill rates of the structure at those higher incidence angles. (702)