Future fuels will come from a variety of feed stocks and refinement processes. Understanding the fundamentals of combustion and pollutants formation of these fuels will help clear hurdles in developing flex-fuel combustors. To this end, we investigated the combustion, soot formation, and soot oxidation processes for various classes of fuels, each with distinct physical properties and molecular structures. The fuels considered include: conventional No. 2 diesel (D2), low-aromatics jet fuel (JC), world-average jet fuel (JW), Fischer-Tropsch synthetic fuel (JS), coal-derived fuel (JP), and a two-component surrogate fuel (SR). Fuel sprays were injected into high-temperature, high-pressure ambient conditions that were representative of a practical diesel engine. Simultaneous laser extinction measurement and planar laser-induced incandescence imaging were performed to derive the in-situ soot volume fraction. From experiments, it was found that fuels with long lift-off length generally produce less soot but fuel molecular structure also affects soot formation. For instance, JP fuel with the longest lift-off length among tested fuels showed higher soot than JS because of higher cycloparaffinic content. Attributed to variations in both lift-off length and molecular structure, the level of total soot within the fuels jet in decreasing order was D2=SR≻JW≻JP≻JC≻JS. Further details of the soot processes were clarified by sampling the soot particles from within the reacting jet by means of a thermophoretic probe, with subsequent analysis by transmission electron microscopy (TEM). Analyzed TEM images of soot particles showed a marked variation in the soot particle structures depending on the fuel type and were consistent with the soot volume fraction trend.