Semiconductor devices, methods of manufacture thereof, and packaged semiconductor devices are disclosed. In one embodiment, a method of manufacturing a semiconductor device includes forming a plurality of contact pads over a substrate, and forming an insulating material over the plurality of contact pads and the substrate. The insulating material is patterned to form an opening over each of the plurality of contact pads, and the plurality of contact pads is cleaned. The method includes forming an under-ball metallization (UBM) structure over the plurality of contact pads and portions of the insulating material. Cleaning the plurality of contact pads recesses a top surface of each of the plurality of contact pads.