A method is provided for programming step and repeat operations of a machine vision inspection system. The machine vision inspection system includes an imaging portion, a stage for holding one or more workpieces in a field of view (FOV) of the imaging portion, a control portion, and a graphical user interface (GUI). According to the method, a user operates the machine vision inspection system to define a set of inspection operations to be performed on a first configuration of workpiece features. The user also operates the GUI to display a step and repeat dialog box, in which he defines a first plurality of parameters defining a set of default step and repeat locations for performing the defined set of inspection operations. The user further operates the GUI to define a set of inspection step and repeat locations, which is a subset of the defined set of default step and repeat locations, where the inspection operations are to be actually performed.