The mechanism of self-assembly of 140 peptide amphiphiles (PAs) to give nanofiber structures was investigated using a coarse-grained method to quantitatively determine whether the assembly process involves discrete intermediates or is a continuous process. Two novel concepts are introduced for this analysis, a cluster analysis of the time dependence of PA assembly and use of the fraction of native contacts as reaction coordinates for characterizing thermodynamic functions during assembly. The cluster analysis of the assembly kinetics demonstrates that a pillar-like intermediate state is formed before the final cylindrical semifiber structure. We also find that head group assembly occurs on a much shorter time scale than tail group assembly. A 2D free-energy landscape with respect to the fraction of native contacts was calculated, and the pillar-like intermediate structure was also found, with free energies about 1.2 kcal/mol higher than the final state. Although this intermediate state exists for only hundreds of nanoseconds, the PA self-assembly process can be recognized as involving two steps, (a) transition from the disordered state to the noncylindrical pillar-like intermediate and (b) pillar-like to final semifiber transition. These results are important to the further design of PAs as functional nanostructures.