Abstract: Methods of manufacturing calibration wafers by forming a first layer of a material on a layer of a substrate material. In a first embodiment, calibration spheres are deposited on the first layer of material followed by an etch process that removes exposed portions of the first layer of a material. The calibration spheres are removed leaving pillars of the first layer of a material formed on the layer of a substrate material. The calibration spheres can be of various sizes forming pillars of various sizes. The calibration wafer with the various size pillars is scanned in a scan tool to determine the scan tool sensitivity. In a second embodiment, a layer of a second material is deposited on and around the various size pillars forming bumps over the various size pillars.