A method for performing high-speed focus height measurement operations in a machine vision inspection system comprising an illumination source and an imaging system that comprises a variable focal length lens and a camera system comprising an electronic rolling shutter and a pixel array, the method comprising: placing a workpiece in a field of view of the machine vision inspection system; determining a region of interest for focus height measurement operations; operating the illumination source to illuminate the workpiece with strobed illumination; controlling the variable focal length lens to periodically sweep a range of focal lengths at a focus modulation frequency, in order to periodically modulate a focus position of the imaging system to sweep a range of focus positions at the focus modulation frequency along a Z-height direction proximate to the workpiece; collecting an image stack comprising respective images focused at respective Z heights, including moving the field of view relative to the workpiece along a direction of motion parallel to a pixel orientation of the camera system and collecting images of the image stack as the field of view moves, wherein each image of the image stack is a stripe of the pixel array with a width along the direction of motion equal to at least one portion of the region of interest, and wherein each image of the image stack is exposed using an instance of strobed illumination timed to correspond with a respective phase of the periodically swept focus position that corresponds to a respective Z height within the image stack; and determining a Z-height measurement for the at least one portion of the region of interest based on analyzing the image stack to determine a Z height corresponding to a best focus position for the at least one portion of the region of interest. placing a workpiece in a field of view of the machine vision inspection system; determining a region of interest for focus height measurement operations; operating the illumination source to illuminate the workpiece with strobed illumination; controlling the variable focal length lens to periodically sweep a range of focal lengths at a focus modulation frequency, in order to periodically modulate a focus position of the imaging system to sweep a range of focus positions at the focus modulation frequency along a Z-height direction proximate to the workpiece; collecting an image stack comprising respective images focused at respective Z heights, including moving the field of view relative to the workpiece along a direction of motion parallel to a pixel orientation of the camera system and collecting images of the image stack as the field of view moves, wherein each image of the image stack is a stripe of the pixel array with a width along the direction of motion equal to at least one portion of the region of interest, and wherein each image of the image stack is exposed using an instance of strobed illumination timed to correspond with a respective phase of the periodically swept focus position that corresponds to a respective Z height within the image stack; and determining a Z-height measurement for the at least one portion of the region of interest based on analyzing the image stack to determine a Z height corresponding to a best focus position for the at least one portion of the region of interest.