A method comprises: using a Scanning Electron Microscope (SEM) to acquire an image of a specimen; identifying one or more objects of interest within the SEM image; generating a scan mask indicating a first set of one or more regions corresponding to the identified one or more objects of interest; and based on the scan mask, providing instructions to the SEM to acquire one or more Electron Backscatter Diffraction (EBSD) images from the first set of one or more regions of the specimen, wherein the method is performed by at least one device including a hardware processor.