A scanning electron microscopy system for mitigating charging artifacts includes a scanning electron microscopy sub-system for acquiring multiple images from a sample. The images include one or more sets of complementary images. The one or more sets of complementary images include a first image acquired along a first scan direction and a second image acquired along a second scan direction opposite to the first scan direction. The system includes a controller communicatively coupled to the scanning electron microscopy sub-system. The controller is configured to receive images of the sample from the scanning electron microscopy sub-system. The controller is further configured to generate a composite image by combining the one or more sets of complementary images.