Electron projection lithography (EPL) has high-resolution capability of meeting the 65 nm technology node and beyond. A first-generation EPL has been developed and improved at Nikon and Selete. Defect free mask is indispensable for successful introduction of this technology into the production stage. However, an EPL mask is considerably different from today's optical photomask, especially due to its 3-D structure. Hence the conventional methods of quality assurance used for optical photomask are not applicable for EPL mask. Selete is now developing a series of defect inspection and repair systems for an EPL stencil mask infrastructure. In our previous work we reported on the individual systems for defect inspection and mask repair by using programmed defects. Moreover, we verified a number of the defect inspection and repair systems through a sequential process. In this work the motivation is to investigate relationship issues among these tools for future applications, such as defect printability, CD controllability, calibration, optimization, performance matching, and automated operation.