Self-organization by the directed migration of components within a system is an important process in many applications, such as the unidirectional migration of motor proteins for transporting items to specific sites in a cell. This manuscript describes a class of functional polymeric molecules that have a set of instructions written by specific chemical moieties. These instructions allow the functional polymeric molecules to be used for autonomous synthesis of particles: particles with both functional core-shell structure and customizable shapes are fabricated for the first time. The functional polymeric molecules direct the large-scale migration of the liquid molecules to specific sites for forming the required customized structure of the particle, thus overcoming previous challenges of fabricating this class of particles. This first synthesis of this class of particles enables the development of novel applications: the concept of shape specificity for targeting sites. Both the basic structural properties (core-shell structure and customizable shape) are used in the specific applications of targeted drug delivery and imaging. The secure physical fit due to the complementary shapes enables the particles to remain locked in position for the targeting. Polymeric molecules are first shown to be highly capable of being encoded with instructions for autonomous synthesis of structured materials.