Mask blanks for extreme ultraviolet lithography (EUVL) are fabricated by depositing Mo/Si multilayer films on 6" square super polished substrates. These mask blanks must be almost defect-free and development of a suitable multilayer deposition tool and process is crucial for the commercialization of EUVL. We will show that using current, real-world quartz substrates and our state-of-the-art defect inspection tool, that substrate defect decoration is an obstacle; this means that there appear to be many non-detectable substrate defects that become detectable once a reflective coating is deposited. This makes it very challenging to conduct accurate defect root cause analysis experiments. We have overcome this obstacle: it entails characterizing an already coated substrate for defects, which provides a suitable reference from which to measure the defects in the multilayer coating that is subsequently applied. We will demonstrate that this is a viable technique and that it enables a suitable defect baseline to be obtained; this is crucial to performing accurate root cause analysis experiments for potential defect sources/mechanisms.