1. A method comprising: receiving a mask design database, wherein the mask design database corresponds to a mask and has a die area, and wherein the mask design database contains a mask database feature disposed within the die area; receiving a mask image corresponding to the mask; comparing the mask image to the mask design database to determine mask defect information corresponding to a mask defect not related to mask alignment using a comprehensive inspection system; comparing the mask image to the mask design database to determine a database-to-mask offset using a computer of the comprehensive inspection system; determining a mask overlay characteristic from the database-to-mask offset; and determining a mask alignment factor from the mask overlay characteristic, wherein the mask alignment factor is for use in adjusting the mask position during photolithography.