A sample inspection system has line sensors that generate sample picture data for layers of a sample disposed at different depths of the sample. The line sensors are arranged parallel to each other and displaced from each other in a vertical direction relative to the sample. A lens system focuses the layers of the sample at the different sample depths on the respective line sensors so that pictures of the layers at the different sample depths are read as line picture data by the line sensors. The sample inspection system includes an apparatus that stores the generated sample picture data, allows a planar region of the sample to be designated by a user for display, extracts picture data corresponding to the designated planar region for each of the sample layers from the sample picture data in response to designation of the planar region, and stores the extracted picture data as a set. An image processing apparatus displays on a display pictures corresponding to the extracted picture data of the respective layers by one of selectively displaying each picture individually in an alternating manner and simultaneously displaying two or more of the pictures together in a parallel or superposed manner.