A surgical site is simultaneously illuminated by less than all the visible color components that make up visible white light, and a fluorescence excitation illumination component by an illuminator in a minimally invasive surgical system. An image capture system acquires an image for each of the visible color components illuminating the surgical site and a fluorescence image, which is excited by the fluorescence excitation component from the illuminator. The minimally invasive surgical system uses the acquired images to generate a background black and white image of the surgical site. The acquired fluorescence image is superimposed on the background black and white image, and is highlighted in a selected color, e.g., green. The background black and white image with the superimposed highlighted fluorescence image is displayed for a user of the system. The highlighted fluorescence image identifies tissue of clinical interest.