A method of measuring a lower similar layer that is separated from an upper similar layer by an intervening dissimilar layer in an integrated circuit. A first electron beam having a first relatively lower landing energy is directed at the integrated circuit. The first relatively lower landing energy is sufficient to completely penetrate the upper similar layer and insufficient to completely penetrate the intervening dissimilar layer, thereby producing first readings that are characteristic of the upper similar layer. A second electron beam having a second relatively higher landing energy is directed at the integrated circuit, the second relatively higher landing energy is sufficient to completely penetrate the upper similar layer, the intervening dissimilar layer, and the lower similar layer, thereby producing second readings that are characteristic of both the upper similar layer and the lower similar layer. The first readings that are characteristic of the upper similar layer are subtracted from the second readings that are characteristic of both the upper similar layer and the lower similar layer, to produce third readings that are characteristic of only the lower similar layer.