Nanoparticles have a wide range of applications due to their unique geometry and arrangement of atoms. For a precise structure-property correlation, information regarding atomically resolved 3D structures of nanoparticles is utmost beneficial. Though modern aberration-corrected transmission electron microscopes can resolve atoms with the sub-angstrom resolution, an atomic-scale 3D reconstruction of a nanoparticle using Scanning Transmission Electron Microscopy (STEM) based tomographic method faces hurdles due to high electron irradiation damage and “missing-wedge”. Instead, inline 3D holography based tomographic reconstructions from single projection registered at low electron doses is more suitable for defining atomic positions at nanostructures. Nanoparticles are generally supported on amorphous carbon film for Transmission Electron Microscopy (TEM) experiments. However, neglecting the influence of carbon film on the tomographic reconstruction of the nanoparticle may lead to ambiguity. To address this issue, the effect of amorphous carbon support was quantitatively studied using simulations and experiments and it was revealed that increasing thickness and/or density of carbon support increases distortion in tomograms. © 2020 Elsevier B.V.