Composite materials, and carbon fiber reinforced plastics (CFRP) in particular, are nowadays widely used in the design of high performance aeronautical and aerospace lightweight structures. Applications to other sectors have, however, been limited due to their high costs and long processing times. To address these issues, the CETIM has developed the Quilted Stratum Process (QSP); a fully automated high-volume production line of thermoplastic composite parts. The QSP manufactures variable-thickness and variable-stiffness composite laminates by assembling composite layers of various orientations and shapes. The focus of this work is to bring together the great versatility of composite design offered by the QSP under a single coherent framework, automating and simplifying the design of QSP-manufactured structures. To this end, we develop the Quilted Stratum Design (QSD). The QSD is a three-step laminate optimization procedure during which the structure is first ideally optimized, then simplified and finally detailed layer by layer to be interpreted for QSP-manufacturing. The method is presented in this paper and applied to both an academic and an industrial case study for which the trade-off between the manufacturing complexity and mechanical performances is studied. In both our applications, partitioning the structure into small numbers of constant stiffness areas was found to be sufficient to significantly over-perform conventional constant stiffness designs and well-compatible with the QSP.