Semiconductor device packaging methods and structures thereof are disclosed. In one embodiment, a method of packaging semiconductor devices includes coupling a plurality of second dies to a top surface of a first die, and determining a distance between each of the plurality of second dies and the first die. The method also includes determining an amount of underfill material to dispose between the first die and each of the plurality of second dies based on the determined distance, and disposing the determined amount of the underfill material under each of the plurality of second dies.