Methods for locating and characterizing defects can include performing a first scan of a substrate to produce a first defect map including a first set of coordinates of one or more defects of the substrate and performing a second scan of one or more regions of the substrate associated with the defects based on the first defect map to produce one or more electron channeling contrast (ECC) images of the defects. Characterization of the defects can be based on the ECC images alone or in combination with other techniques. Such methods can include determining a second set of coordinates associated with the one or more defects based on the ECC images and directing an ion beam toward the substrate and milling the substrate based on the second set of coordinates.