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. In contrast to notable variations of the morphology, the obtained fringe length and tortuosity were almost constant, regardless of the fuel aromatic contents and the in-flame locations. The fringe separation slightly decreased towards downstream in the flame, likely due to annealing of carbon graphenes in increasing temperature confirmed by in-flame thermocouple measurements. The variations in fringe separation did not show significant difference with fuel aromatic contents. On the other hand, the in-cylinder to exhaust variations of soot nanostructure from engine experiments in a literature were found to be significantly larger than the in-flame variations obtained in the present study suggesting the significance of late-cycle in-cylinder soot oxidation, although the difference in the experimental conditions should be kept in mind.