A wafer inspection method is provided. The wafer inspection method includes identifying a plurality of candidate regions on an image of a DUT on a wafer; generating a confidence score for each of the plurality of candidate regions, wherein the confidence score indicates a probability of a candidate region including a probe mark; selecting a first candidate region having the highest confidence score as a selected region; determining whether a second candidate region in the plurality of candidate regions includes the same probe mark as the first candidate region; and eliminating the second candidate region if the second candidate region includes the same probe mark as the first candidate region.