A method includes directing an ion beam at a plurality of differing incident angles with respect to a target surface of a substrate to implant ions into a plurality of portions of the substrate, wherein each one of the plurality of differing incident angles is associated with a different one of the plurality of portions, measuring angle sensitive data from each of the plurality of portions of the substrate, and determining an angle misalignment between the target surface and the ion beam incident on the target surface from the angle sensitive data. A method of determining a substrate miscut is also provided.