In this article, the diverse morphologies observed after annealing or crystallization from the melt in P(VDF-ter-TrFE-ter-CTFE) terpolymers with varying CTFE amounts were explained through a combination of AFM and SAXS experiments. The very significant and, so far, unexplained evolution of the SAXS spectra after annealing above the Curie transition was interpreted by the formation, during annealing, of semi-crystalline domains without a significant evolution of the crystalline lamellar period. The morphologies obtained after crystallization from the melt were also explained and the coexistence of two periodic stacks (with period around 30–40 nm and 14–18 nm) was shown. Low cooling rates and CTFE amounts create long and thick semi-crystalline domains with a well-defined orientation, while high cooling rates and CTFE amounts create thinner and shorter domains without a predominant orientation. The AFM images showed that the periodic organization of the crystalline lamellae with a period, LP, around 15 nm is maintained, regardless of the crystallization process used (solvent cast, annealed, or melt-crystallized). The combined AFM/SAXS method used in this study can be applied to other semi-crystalline polymers.