1. A mask pattern inspection method comprising: transferring a mask pattern onto a conductor substrate or a semiconductor substrate; preparing a sample comprising a substrate surface pattern in an electrically conductive state to the substrate, and in a shape in accordance with the transferred mask pattern; irradiating the sample with an electron beam to detect at least one of a secondary electron, a reflected electron and a backscattered electron generated from the surface of the sample, thereby acquiring an image of the sample surface; and inspecting the mask pattern on the basis of the image, wherein the substrate surface pattern comprises one of a first pattern formed by selectively removing an insulating layer above the substrate, a second pattern formed by selectively removing a conductive layer on an insulating layer above the substrate, and a third pattern formed by filling a pattern formed by selectively removing a surface layer of the substrate, with an insulating material, and incident energy of the electron beam onto the sample and a thickness of the insulating layer or of the third pattern are selected in a manner that the electron beam penetrates the insulating layer or the insulating material to reach a layer beneath the insulating layer or the third pattern.