A method and system for measuring layer overlay and for inspecting a mask for defects unrelated to overlay utilizing a singe comprehensive tool is disclosed. An exemplary method includes receiving a mask design database that corresponds to a mask and has a die area with a mask database feature. A mask image of the mask is received, and a comprehensive inspection system compares the mask image to the mask design database in order to detect mask defects that are not related to layer alignment. The system produces mask defect information corresponding to the mask defects. The comprehensive inspection system also compares the mask image to the mask design database to determine a database-to-mask offset. From the database-to-mask offset, a mask overlay characteristic is determined.