We analyze the behavior of Free Electron Laser (FEL) oscillators operating in the deep saturated regime and point out the formation of sub-peaks of the optical pulse. They are very stable configurations, having a width corresponding to a coherence length. We speculate on the physical mechanisms underlying their growth and attempt an identification with FEL mode locked structures associated with Super Modes. Their impact on the intra-cavity nonlinear harmonic generation is also discussed along with the possibility of exploiting them as cavity out-coupler.