The scattering of atomic and molecular beams from well-characterized surfaces is a useful method for studying the dynamics of gas-surface interactions, providing precise information on the energy and momentum exchange which occur in such encounters. We apply this technique to new systems including disordered films of macromolecules, complex interfaces of macromolecular systems, and hybrid organic-semiconductor interfaces. Time-lapse atomic force microscopy studies of diblock copolymer structural evolution and fluctuations complement the scattering data to give a more complete understanding of dynamical processes in these complex disordered films. Our new scattering findings quantitatively characterize changes in interfacial dynamics including confinement in thin films of poly(methyl methacrylate) and changes in the physical properties of poly(ethylene terephthalate) films as they transform from the glassy to their semicrystalline phase. Further measurements on a hybrid organic-semiconductor interface, methyl-terminated silicon (111), reveal that the surface thermal motion and gas-surface energy accommodation are dominated by local molecular vibrations while the interfacial lattice dynamics remain accessible through helium scattering. High temperature atomic force microscopy allows direct, real-time visualization of structural reorganization and defect migration in poly(styrene)-block-poly(methyl methacrylate) films, revealing details of film reorganization and thermal annealing. Moreover, we employed lithographically created channels to guide the alignment of polymer microdomains. This, in turn, allows direct observation of the mechanisms for diffusion and annihilation of dislocation and disclination defects. In summary, this paper elaborates on the power of combining atom scattering and scanning probe microscopy to interrogate the vibrational dynamics, energy accommodation, energy flow, and structural reorganization in complex interfaces.