A pattern inspection apparatus can be provided, for example, in a scanning electron microscope system. When patterns of a plurality of layers are included in a SEM image, the apparatus separates the patterns according to each layer by using design data of the plurality of layers corresponding to the patterns. Consequently, the apparatus can realize inspection with use of only the pattern of a target layer to be inspected, pattern inspection differently for different layers, or detection of a positional offset between the layers.