An electron microscope suitable for observing at least one sample is provided. The sample has at least one testing area, and a material of the sample on the testing area is semiconductive or conductive. The electron microscope includes a stage, an electron gun, and at least one probe. The stage is suitable for carrying the sample and the sample is not electrically grounded. The electron gun is suitable for generating an electron beam and accumulating charges on the sample. When the probe contacts with the testing area, the image contrast of the testing area will change. The current through the probe will also change upon contact. Methods have been provided based on these principles to determine “when” and “where” the probe starts to contact the sample surface inside an electron microscope.