For accurate nm-figure error correction of EUV multilayer mirror optics, a three-dimensionally controlled ion milling method was developed. To demonstrate the reflection phase manipulation of an EUV multilayer, 10 periods of a 40-period Mo/Si multilayer were partially removed. A partially milled Mo/Si multilayer with a contact double slit was successfully fabricated for interference fringe observations, which were carried out using a Young's EUV interferometer with a reflection configuration. The fringe pattern revealed a small reflection phase change after multilayer surface milling. EUV interferometry results demonstrated the effectiveness of the proposed method for sub-nanometer digital wavefront error correction in the case of multilayer mirror optics used in diffraction-limited imaging.