We describe the characterization of native phase defects in the manufacturing of extreme ultraviolet (EUV) mask blanks using the state-of-the-art mask metrology equipment in SEMATECH's Mask Blank Development Center (MBDC). We used commercially available quartz substrates and deposited Mo/Si multilayers on the substrates to characterize phase defects. We also prepared programmed defects of various dimensions using e-beam patterning technology on which multilayers were deposited. Transmission electron microscopy (TEM) was used to study multilayer profile changes, while SEMATECH's actinic inspection tool (AIT) was used to image defects and predict their printability. Defect images at different focal depths of the AIT are correlated to TEM cross sections and atomic force microscopy (AFM) dimensions. The printability of native and programmed defects was also investigated.