The present invention relates to a process for obtaining a system for the controlled delivery of a biologically active substance allowing to obtain an effective delivery in terms of percentage of said biologically active substance that is absorbed by the organism. More particularly, the present invention relates to a process consisting in obtaining a controlled delivery system in which the biologically active substance is enclosed in a structure having a substantially parallelepiped shape with the desired shape and size, which can internally adapt to the biologically active substance to be carried and externally to the interaction with target cells (for example, enterocytes), thus optimizing the delivery modes of said biologically active substance. Advantageously, the process according to the invention allows to create parallelepiped structures with nanometric, micrometric or larger sizes, thereby making the controlled delivery system thus obtained suitable for a large variety of biologically active substances, including ions, molecules and macromolecules.