Precise interpretation of three-dimensional atom probe tomography (3D-APT) data is necessary to reconstruct semiconductor-device structures. In particular, it is difficult to reconstruct the hetero-structure of conductors and insulators using APT analysis, due to the preferential evaporation of low-evaporation field-material. In this paper, shallow-trench isolation (STI) structure, consisting of a Si column and a SiO2 region, is analyzed using APT. The dimensional artifact known as the local-magnification-effect occurring as a result of the geometric deviation from the ideal hemisphere was successfully calibrated by ‘high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) tomography’ and Electron Energy Loss Spectroscopy (EELS). In the direction of the width, the Si layer was compressed by 50%, and the interface was expanded by 250% with respect to the reference data obtained for the same sample. A 5-nm-thick transition layer was observed at the interface between Si and SiO2. The composition of the transition layer follows the well-developed sequence Si-Si2O-SiO-SiO2 from the Si area to the SiO2 area. Atoms at the interface were likely to evaporate with a bit wider angle than atoms in the Si area due to the preferentially evaporated Si layer, which caused the interface area to appear locally magnified.