A method of using an in-situ aerial image sensor array is disclosed to separate and remove the focal plane variations caused by the image sensor array non-flatness and/or by the exposure tool by collecting sensor image data at various nominal focal planes and by determining best focus at each sampling location by analysis of the through-focus data. In various embodiments, the method provides accurate image data at best focus anywhere in the exposure field, image data covering an exposure-dose based process window area, and a map of effective focal plane distortions. The focus map can be separated into contributions from the exposure tool and contributions due to topography of the image sensor array by suitable calibration or self-calibration procedures. The basic method enables a wide range of applications, including for example qualification testing, process monitoring, and process control by deriving optimum process corrections from analysis of the image sensor data.