The aim of this work was to compare the fractal characteristics, D_f and k_f, the primary particle diameter, D_pp, the gyration diameter of aggregates, D_g, and the overlap coefficient, C_ov, of carbon nanoparticle aggregates produced by an ethylene diffusion flame and sampled by means of four commonly used techniques. The first method involves a thermophoretic piston probe (TPP) which inserts a TEM grid into the flame. Three other methods were applied at the outlet of a dilution device, also inserted in the flame. The first of these used a nuclepore filtration sampler (NFS), and is based on filtration of particles onto a polycarbonate membrane. The second, post dilution method, the insertion particle sampler (IPS), inserts a TEM grid, perpendicular to the aerosol flow. Similar to TPP, the last method is a thermophoretic particle sampler (TPS) sampling directly onto a TEM grid. After collection, the samples are stored in the dark either, (1) in a nitrogen filled cell at low humidity or, (2) in ambient air for studying atmospheric ageing. Good agreement was observed between TPP, TPS, and IPS indicating that the dilution induced for TPS and IPS does not significantly change the morphology of soot. On the other hand, the NFS protocol tended to overestimate the overlap coefficient and the size of primary particles and aggregates. Finally, with regard to the aging effect, we found that k_f and D_pp evolve slowly during storage in the atmosphere while D_f, was insensitive to the storage conditions. However, the overlap coefficient increased and the gyration diameter decreased as a function of storage duration, while storage under nitrogen tended to reduce these changes.