It is very difficult to predict how multilayer defects known as “phase defects” impact on wafer printed image when embedded in an extreme ultraviolet (EUV) mask. Therefore, researchers have reported many techniques to analyze and characterize phase defects using scanning probe microscopes (SPMs) and phase defect inspection tools that employ deep ultraviolet or EUV optics. To characterize the phase defects using SPM or other inspection tools, preparing and employing a programmed phase defect mask is a practical way to address the task because the locations, sizes, and quantity of phase defects can be defined to fit experiments. For this study, a programmed phase defect mask was prepared to investigate the size uniformity of the programmed phase defects. The designed phase defects were holes 40-, 50-, 70-, or 80-nm-wide and 4.5-nm-deep. Using a SPM, the phase defects were measured for their depths and widths before and after coating with the multilayer. As a result, variations in the measured depths and widths were much smaller than the defect-to-defect variations, reflecting measurement repeatability. In addition, the variations in the depths and widths of the phase defects after multilayer coating were larger than before coating. It was also found that a given group of phase defects exhibited significant variations in depth and width after multilayer coating, even if they were the same prior to coating. This result indicated that it is difficult to estimate precoating phase defect sizes based on measurements after the multilayer is coated.