A method and apparatus for generating an image of a specimen with a scanning electron microscope (SEM) is disclosed. The SEM has a source unit for directing an electron beam substantially towards a portion of the specimen, a detector for detecting particles that are emitted from the specimen, and an image generator for generating the image of the specimen from the emitted particles. The image features are controlled by conditions under which the image is generated. The specimen is scanned under a first set of conditions to generate a first image during a first image phase. The specimen is then scanned under a second set of conditions during a setup phase. The second set of conditions are selected to control charge on the specimen. The specimen is then scanned under the first set of conditions to generate a second image during a second image phase. The features of the second image are controlled by the first and second sets of conditions.