1. A method of generating a composite image of a non-flat surface of a test object using a microscope, the method comprising: acquiring, using the microscope, a plurality of three-dimensional images of different areas of the non-flat surface, where each image comprises a region of overlap with at least one adjacent image, the microscope having sufficient resolution to image in three dimensions a microstructure on the non-flat surface having a lateral dimension of 10 microns or less and a height of 10 nm or less; determining, for each of the images, a set of rigid body parameters relating a position and an orientation of the test object in the image to a common coordinate system, where the set of rigid body parameters is determined by fitting the resolved microstructure in the overlap region in the image with the corresponding microstructure in the overlap region of the adjacent image; and combining the plurality of images based on the sets of rigid body parameters to generate a composite image of the surface.