The formation of two-dimensional (2D)-hexagonal (p6m) silica-based hybrid materials from concentrated micellar solutions (10 wt %) of two nonionic fluorinated surfactants, R(7)(F)(EO)(8) and R(8)(F)(EO)(9), is investigated in situ using synchrotron time-resolved small angle X-ray scattering (SAXS). The two surfactants form direct micelles with different structures prior to the silica precursor addition as demonstrated by SAXS and SANS. R(8)(F)(EO)(9) gives spherical micelles and R(7)(F)(EO)(8) more complex ones, modeled here as short wormlike micelles. The in situ SAXS experiments reveal that both surfactants form well-ordered 2D-hexagonal hybrid materials after the addition of the silica precursor, in coexistence with an excess of surfactant micelles. The structures of both 2D-hexagonal phases are compared just after precipitation, and it is found that more robust and larger silica walls are formed for R(8)(F)(EO)(9) than for R(7)(F)(EO)(8). This could explain why only the material obtained with R(8)(F)(EO)(9) is stable upon washing, as observed previously. Moreover, it is proposed that in both cases, only a part of the micelles interact with the silica oligomers and undergo structural modifications before forming the 2D-hexagonal mesophase. The obtained results are finally discussed in the more general framework of the templating mechanism for nonionic surfactants.