A method improves focus height repeatability in a machine vision inspection system. A region of interest is defined within a field of view imaged by a camera portion, wherein an aligned edge feature in the region of interest may introduce a focus height sensitivity that varies depending on the aligned edge feature offset relative to the image pixels. A first set of focus-determining operations determines a focus height for the region of interest, and comprise at least one of: (a) operations that reduce the sensitivity of the focus height determination to the offset of the aligned edge feature relative to the image pixels; and (b) operations that adjust the offset of the aligned edge feature relative to the image pixels according to a predetermined offset repeatability criteria, such that the image data used in the focus height determination fulfills the offset repeatability criteria.