System and method for incorporating user input on the fly during an otherwise automatic registration process. During rigid registration, user input adjusts the current computed pose or transformation that relates the two images being aligned. During warping, user input adjusts the flow field locally, and is gradually smoothed into the surrounding flow field. During multi-scale registration where images are first aligned at a course resolution, and subsequently at progressively finer resolutions, user input is applied at the current scale. User input is detected during the automated process either by interrupts or polling. Between user inputs the registration results are re-rendered.