A method of inspecting for plug-to-plug short (short circuit) defects on a sample is disclosed. A charged particle beam for imaging the sample is repeatedly line-scanned over the sample with a line-to-line advancement direction perpendicular to the line-scan direction. The method includes scanning the sample with a line-to-line advancement along a first and a second direction, to obtain a first and a second image of the sample, respectively. Then, the method includes identifying plug patterns, represented in the obtained images with abnormal grey levels, as abnormal plug patterns. Next, the method compares the locations of the abnormal plug patterns to determine the presence of plug-to-plug short defects on the sample.