A method for estimating an in-focus position of a target using an image scanning apparatus is provided. The in-focus position is monitored at a seed location and an end location on the target and a pre-scan path is calculated between these locations. A pre-scan is then performed and a focus parameter is monitored for a plurality of locations along the pre-scan path. An imaging scan is next performed wherein the target is imaged along an image scan path and a focus parameter is monitored for a plurality of locations along said path. The focal height of the apparatus is adjusted during the imaging scan by comparing the focal parameter monitored for a current location on the image scan path with the focal parameter monitored for a similar location on the pre-scan path. The focal parameter monitored for different locations on the image scan path may also be compared.