Materials with highly ordered nanoscale structures can translate molecular processes to macroscopic function. Here we report on the photo-controlled organization of achiral alternating copolymers composed of discrete length blocks showing well-defined sub-10 nm morphologies. These alternating copolymers consist of main-chain azobenzene building blocks alternating with discrete oDMS blocks of various precise lengths. Remarkably, we demonstrate the imprinting of a stable helical molecular arrangement in spin-casted thin films by irradiation with circularly polarized light, without chiral dopant or plasticizer required. By following the out-of-equilibrium photo-switching process over irradiation time, the mechanism of molecular reorganization is unraveled and rationalized with the nature of the morphology. Linear photo-organization is preferentially reached with flexible and symmetric cylindrical structures while helical photo-organization is most easily obtained with robust but rotatable lamella structures. These findings suggest that precision in the synthesis and assembly of alternating copolymers can lead to complete control over molecular organization and main-chain motion.