We have probed the mechanical properties of purple membrane (PM) in a physiological environment using the atomic force microscope (AFM). By suspending PM over nano-trenches, the elastic properties of PM can be evaluated free from the interaction with the substrate. Force-displacement curves were obtained on the suspended membrane and the data was compared to that of a simple model of a thin film over a trench. By fitting the data to the model, the elastic modulus of PM was estimated to be 8 MPa. When the membrane is repeatedly indented, we observed a change in the force-distance data consistent with damage to the two-dimensional crystal of PM. In this paper we demonstrate that the AFM allows us to evaluate the mechanics of biological membranes in their native conditions. (C) 2008 Elsevier B.V. All rights reserved.