Atomic force microscopy (AFM) is widely used to image biological nanostructures. In this work, we demonstrate that AFM can be used to quantitatively characterize the polymorphism of amyloid fibrils through an analysis of height histogram plots under conditions where the image lacks high lateral resolution. In this approach, Gaussian fits are used to determine the characteristic height and volume of fibril species in the height-histogram plot of an image, and to convert these distributions into a quantitative assessment of the relative volume content of various species. This approach to fibril analysis facilitates rapid quantitative analysis of polymorphic species in heterogeneous samples of amyloid fibrils and other nano-structured materials.