Atomic force microscopy can be used to determine the vertical dimension of biological molecules under native conditions with high resolution. Deformation of soft proteins by the scanning force, however, introduces error in the magnitude of the measurement. In this work, the force-dependent height of NADPH-cytochrome P450 reductase, an integral membrane protein, was measured by atomic force microscopy and analyzed to account for the contribution of deformation to the observed height of the molecule above a model membrane surface. Imaging of single reductase molecules was accomplished by reconstitution into 10 nm diameter phospholipid bilayer particles, which provides a way of adsorbing the protein-phospholipid complex on a surface in the proper orientation. The results show that the height of the reductase is drastically underestimated in contact imaging mode. An analysis of force curves taken on single reductase molecules provides a height; that better matches the known dimensions of the protein. This technique should be generally useful for determining the vertical dimension of biological samples that are severely deformed by contact imaging forces.