Atomic force microscopy has developed into a powerful tool in the study of phase separation in lipid bilayers. Its ability to image a semi-fluid surface under buffer at nanometre lateral resolution and Angstrom resolution vertically allows us to distinguish phase separated lipid domains, models of the elusive rafts postulated to exist as functional platforms in the cellular membrane, which may only rise 0.3 nm above the surrounding membrane. This review charts the history of this development, and includes a description of sample preparation techniques, factors affecting image contrast mechanisms, its use in the investigation of the pre-transition ripple phase, and in the localization of cell surface proteins.