We synthesized hydrophilic and hydrophobic carbon nanoparticles (CNPs) by femtosecond laser (0.8¯m, 40 fs) irradiation of the water layer of an aerated benzene/water (B/W) bilayer solution. Focusing intense femtosecond laser pulses onto water creates a high density of reactive species such as hydroxyl radicals in a well-confined volume; i.e., plasma filament. The properties of the particle surface were controlled simply by adjusting the laser focusing position, the duration between the preparation of B/W bilayer solution and the laser irradiation. The hydrophobic CNPs appeared to be nearly identical in size and morphology to hydrophilic CNPs. Raman spectroscopy revealed that both particles had a graphitic and disordered structure; however, IR spectroscopy clearly showed that the hydroxy group is the origin of the hydrophilicity. The time evolution of particle formation, products in water, and benzene dissolution behavior in water reveals that the surface properties are determined by the concentration of benzene in water. The diluted aqueous benzene solution gave hydrophilic particles; however, the density of particles was much smaller than that formed in B/W bilayer solution. We concluded that the production of denser hydrophilic CNPs in B/W bilayer was achieved by limiting the concentration of benzene in water layer by B/W interface, and by continuously supplying benzene into water layer through B/W interface. We discuss the subsequent reaction mechanism leading to CNPs of different surface characters.