Methods and systems of part programming for machine vision inspection systems are provided, which permit a user to readily define multiple image acquisition operations interspersed with associated image analysis and/or inspection operations during learn mode operations and in the resulting part program image acquisition operations for at least some of the images are arranged into a continuous motion image acquisition sequence that acquires images and stores images in a "non-interspersed" manner in order to increase the throughput of the machine vision inspection system. Image analysis/inspection operations associated with the stored images are performed subsequently by recalling the store images. The programming systems and methods disclosed herein may operate automatically to facilitate rapid programming for a variety of workpieces by relatively unskilled users, wherein the resulting programs include continuous motion image acquisition sequences.