A method for operating an imaging system of a machine vision inspection system to provide an extended depth of field (EDOF) image. The method comprises (a) placing a workpiece in a field of view; (b) periodically modulating a focus position of the imaging system without macroscopically adjusting the spacing between elements in the imaging system, the focus position is periodically modulated over a plurality of positions along a focus axis direction in a focus range including a workpiece surface height; (c) exposing a first preliminary image during an image integration time while modulating the focus position in the focus range; and (d) processing the first preliminary image to remove blurred image contributions occurring in the focus range during the image integration time to provide an EDOF image that is focused throughout a larger depth of field than the imaging system provides at a single focal position.