Electrical interconnects in integrated circuits have shrunk to sizes in the range of 20-100 nm. Accurate measurements of the dimensions of these nanowires are essential for identifying the dominant electron scattering mechanisms affecting wire resistivity as they continue to shrink. We report a systematic study of the effect of line edge roughness on the apparent cross-sectional area of 90 nm Cu wires with a TaN/Ta barrier measured by conventional two-dimensional projection imaging and three-dimensional electron tomography. Discrepancies in area measurements due to the overlap of defects along the wire's length lead to a 5% difference in the resistivities predicted by the two methods. Tomography of thick cross sections is shown to give a more accurate representation of the original structure and allows more efficient sampling of the wire's cross-sectional area. The effect of roughness on measurements from projection images is minimized for cross-section thicknesses less than 50 nm, or approximately half the spatial frequency of the roughness variations along the length of the investigated wires.