Thin films of phase separated polystyrene-b-polyisoprene-b-polystyrene block copolymers were studied by tapping mode atomic force microscopy. The relative contrast in height and phase mode images of the phase separated regions was found to be very sensitive to changes in the operating conditions of the microscope. Contrast variations and reversals were observed for height and phase mode images as a function of the setpoint amplitude ratio and drive frequency. No unique height or phase contrast was observed for the the tri-block copolymer system examined in this study.