The material-dependent manner in which ion damage occurs in AlAs/GaAs heteroepitaxial structures is demonstrated using conventional and high resolution transmission electron microscopy. Both 150keV and 2MeV Si+ ion implants are employed over a wide range of ion doses. Under conditions which yield rapid build-up of lattice damage in GaAs, the AlAs is found to be relatively resistant to structure breakdown. Indeed, the crystalline AlAs exerts a novel protective effect on immediately adjacent regions of the GaAs layers. For high implantation doses amorphous-crystal superlattices are formed in multilayer structures. For the highest ion doses the AlAs lattice begins to be disrupted by a characteristic, boundary-dependent, heterogeneous mechanism. These observations suggest that mobile point defects play a significant role in AlAs in situ restructuring processes.