The boom in wireless communications has greatly stimulated research in compound semiconductors in recent years. Exciting new advances in materials science has spawned new devices such as High Electron Mobility transistors based on III-Sb materials and quantum dot lasers based on self-assembled 3D islands. The performance of these devices relies to varying degrees on the morphological and compositional uniformity of the layers that make up the devices. Our work centers on understanding the morphological and compositional evolution, as well as the strain relaxation and defect formation in lattice mismatched compound semiconductor thin films. In this talk, I will focus on our work in the area of lateral composition modulation, i.e.; controlled phase separation in multilayer structures. By and large, phase separation is undesirable and has been avoided in device structures. However, reproducibly obtaining regular and robust arrays of phase-separated material is a promising way to acquire low dimensional structures such as quantum dots or wires. We have achieved such arrays by the deposition of short period superlattices, where each layer is on the order of one or two monolayers thick. We have demonstrated lateral composition modulation in several different materials systems, such as GaAs/InAs, AlAs/InAs, and GaSb/GaAs. We have shown that the appearance of lateral composition modulation is correlated to roughening of the surface front. Also, the microstructure is largely dictated by the relative lattice mismatch between the individual superlattice layers. These results are consistent with continuum perturbation models that predict the coupling of morphological and compositional instabilities under the appropriate circumstances.