The atomic force microscope (AFM) has become a useful tool for studying the morphology of membrane surfaces as well as their fouling characteristics. One principle advantage of the AFM over other high resolution imaging techniques is the ability to make observations in both ambient air and liquid environments. Diverse imaging modes also exist, each with their own advantages and disadvantages. In this study two different imaging modes in both air and water are compared when examining two different nanofiltration membranes, to compare the strengths and weakness of different methods of obtaining surface topography when applied to nanofiltration membrane characterization. When imaging the more hydrophobic of the two membranes using tapping mode in a water environment features consistent with the existence of surface adhered nanobubbles were observed. Such features have implications for the fouling of membranes by hydrophobic materials, as well as effects on the ability to image hydrophobic membrane surfaces under such conditions. (C) 2011 Elsevier B.V. All rights reserved.