Semiconductor structures including active fin structures, dummy fin structures, epitaxy layers, a Ge containing oxide layer and methods of manufacture thereof are described. By implementing the Ge containing oxide layer on the surface of the epitaxy layers formed on the source/drain regions of some of the FinFET devices, a self-aligned epitaxy process is enabled. By implementing dummy fin structures and a self-aligned etch, both the epitaxy layers and metal gate structures from adjacent FinFET devices are isolated in a self-aligned manner.