A wafer inspection system is provided. The wafer inspection system includes a memory unit configured to store an image of a device under test (DUT) on a wafer, an image-uploading unit configured to upload the image to a processing unit, and a processing unit. The processing unit is configured to identify a plurality of candidate regions on the image; generate 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; select a first candidate region having the highest confidence score as a selected region; determine whether a second candidate region in the plurality of candidate regions includes the same probe mark as the first candidate region; and eliminate the second candidate region if the second candidate region includes the same probe mark as the first candidate region.