Characterization of soot nanoparticle morphology can be used to develop understanding of nanoparticle interaction with engine lubricant oil and its additives. It can be used to help direct modelling of soot-induced thickening, and in a more general sense for combatting reductions in engine efficiency that occur with soot-laden oils. Traditional 2D transmission electron microscopy (TEM) characterization possesses several important shortcomings related to accuracy that have prompted development of an alternative 3D characterization technique utilizing electron tomography, known as 3D-TEM. This work details progress made towards facilitating semi-automated image acquisition and processing for location of structures of interest on the TEM grid. Samples were taken from a four cylinder 1.4 L gasoline turbocharged direct injection (GTDI) engine operated in typically extra-urban driving conditions for 20,284 km, with automatic cylinder deactivation enabled. Soot nanoparticles were extracted from the used oil drawn from the sump, and prepared on TEM support grids. From a feedstock of chosen grid locations, 30 soot nanoparticles were reconstructed and characterized in 3D and morphological characterization results compared to those derived using 2D-TEM. Results showed significant deviations between the two methods for important morphological parameters such as volume, surface area, and circularity. While volume and circularity were on average underestimated by 23% and 19% respectively, surface area was overestimated by 36%. However, a pixel-based 2D-method for radius of gyration measurements was highly accurate (< 2% deviation on average). Qualitative assessment of complex morphological features, unrecognisable with standard 2D-TEM, was carried out via 3D rendering of soot volumes, highlighting unique outputs of this technique. Presence of morphological features such as bridge-structures and enclosed cavities were observed in numerous particles, and confirmed through observation of tilt-series data.