The availability of defect-free masks is considered to be a critical issue for enabling extreme ultraviolet lithography (EUVL) as the next generation technology. Since completely defect-free masks will be hard to achieve, it is essential to have a good understanding of the printability of EUV mask defects. In this work, two native mask blank defects were characterized using atomic force microscopy (AFM) and cross-section transmission electron microscopy (TEM), and the defect printability of the characterized native mask defects was evaluated using simulations implementing the finitedifference time-domain and the waveguide algorithms. The simulation results were compared with through-focus aerial images obtained at the SEMATECH Berkeley Actinic Inspection Tool (AIT), an EUV mask-imaging microscope at Lawrence Berkeley National Laboratory. The authors found agreement between the through-focus simulation results and the AIT results. To model the Mo/Si multilayer growth over the native defects, which served as the input for the defect printability simulations, a level-set technique was used to predict the evolution of the multilayer disruption over the defect. Unlike other models that assume a constant flux of atoms (of materials to be deposited) coming from a single direction, this model took into account the direction and incident fluxes of the materials to be deposited, as well as the rotation of the mask substrate, to accurately simulate the actual deposition conditions existing inside the ion beam deposition tool. The modeled multilayer growth was compared to the cross-section TEM images through the defects, as well as to the AFM scans for the given defects, and a good agreement was observed between them.