Semiconductor devices and methods of manufacture thereof are disclosed. In a preferred embodiment, a method of manufacturing a semiconductor device includes providing a semiconductor wafer, forming at least one isolation structure within the semiconductor wafer, and forming at least one feature over the semiconductor wafer. A top portion of the at least one isolation structure is removed, and a liner is formed over the semiconductor wafer, the at least one feature, and the at least one isolation structure. A fill material is formed over the liner. The fill material and the liner are removed from over at least a portion of a top surface of the semiconductor wafer.