Layer-by-layer assembly (LbL) is a rich, versatile, and powerful technique for fabricating multilayer thin films with controlled architecture and functions. Singly charged, uncharged, or water-repellent molecules cannot be used directly in conventional LbL assembly. This problem can be solved with unconventional LbL methods, by employing the preassembly of building blocks in solution and the use of these assemblies for LbL formation at the interface. This Concept summarizes different methods of unconventional LbL assembly, including electrostatic complex formation, hydrogen-bonded complexes, block-copolymer micelles, and π–π interaction complexes. These preassembly treatments endow the building blocks with enhanced abilities for advanced functionality, in particular, surface molecular imprinting, a new concept emerging from unconventional LbL. Molecular imprinting approaches are thus conceptually described based on different types of interactions and their great potential in applications is demonstrated by examples such as selective surface patterning and selective filtration.