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In order to examine the effect of fuel aromatics on soot processes in diesel flame, nanostructure and morphology of soot particles directly sampled in a diesel flame were investigated via High-Resolution Transmission Electron Microscopy (HRTEM). Three test fuels with different aromatic contents, aromatic-free Fischer-Tropsch Diesel (FTD), naphthalene-added (65,000ppm) FTD and conventional JIS#2 diesel fuels were used. TEM grids were directly exposed to single-shot diesel flames in a constant volume combustion chamber under a diesel-like condition with EGR (1000K, 2.7MPa, 15%O2) to thermophoretically sample soot particles at different axial locations from 40 to 120mm from nozzle. The soot nanostructure such as length, tortuosity and separation of lattice fringes in primary particles and morphology such as primary particle diameter and aggregate gyration radius were analyzed and compared among different fuels and in-flame locations.