A system, method, and non-transitory computer readable medium are provided for training and applying defect classifiers in wafers having deeply stacked layers. In use, a plurality of images generated by an inspection system for a location of a defect detected on a wafer by the inspection system are acquired. The location on the wafer is comprised of a plurality of stacked layers, and each image of the plurality of images is generated by the inspection system at the location using a different focus setting. Further, a classification of the defect is determined, utilizing the plurality of images.