The generation of nanoscale polymer films using complex, hierarchically structured (bio)macromolecular architectures has important implications in the field of materials science. This study details the surface-confined covalent cross-linking of micellar macrocross-linkers derived from the amphiphilic diblock copolymer, polystyrene-bpoly(N-(2-hydroxypropyl)methacrylamide), via atom transfer radical polymerization (ATRP)-mediated continuous assembly of polymers (CAP(ATRP)), to generate compartmentalized thin films with unique surface morphologies. Using initiator-functionalized silicon wafers, the micellar films were found to be thicker in comparison to thin films prepared from linear macrocross-linkers derived from poly(N-(2-hydroxypropyI)methacrylamide) (15.2 vs 10.2 nm). Unlike the smooth and flat surface morphologies observed for films prepared from the linear macrocross-linker, the micellar films possessed distinctive pitted morphologies that became more pronounced after annealing. Furthermore, the hydrophobic polystyrene cores of the micelles enabled the encapsulation of hydrophobic molecules that subsequently remain compartmentalized during the CAP process, as demonstrated with the encapsulation of the dye Nile Red. The assembly of Nile Red-loaded micelles onto initiator-functionalized silica particles was confirmed via fluorescence microscopy. This study. demonstrates the efficiency and versatility of the CAP approach to generate nanostructured thin films with controllable morphology, surface roughness, thickness, and composition, simply by varying the macromolecular architecture.