Nanometer-scale structuring in room-temperature ionic liquids is observed using molecular simulation. The ionic liquids studied belong to the 1-alkyl-3-methylimidazolium family with hexafluorophosphate or with bis(trifluoromethanesulfonyl)amide as the anions, [C(n)mim][PF6] or [C(n)mim][(CF3SO2)(2)N], respectively. They were represented, for the first time in a simulation study focusing on long-range structures, by an all-atom force field of the AMBER/OPLS_AA family containing parameters developed specifically for these compounds. For ionic liquids with alkyl side chains longer than or equal to C-4, aggregation of the alkyl chains in nonpolar domains is observed. These domains permeate a tridimensional network of ionic channels formed by anions and by the imidazolium rings of the cations. The nanostructures can be visualized in a conspicuous way simply by color coding the two types of domains (in this work, we chose red = polar and green = nonpolar). As the length of the alkyl chain increases, the nonpolar domains become larger and more connected and cause swelling of the ionic network, in a manner analogous to systems exhibiting microphase separation. The consequences of these nanostructural features on the properties of the ionic liquids are analyzed.