A laser annealing method for annealing a stacked semiconductor structure having at least two stacked layers is disclosed. A laser beam is focused on a lower layer of the stacked layers. The laser beam is then scanned to anneal features in the lower layer. The laser beam is then focused on an upper layer of the stacked layers, and the laser beam is scanned to anneal features in the upper layer. The laser has a wavelength of less than one micrometer. The beam size, depth of focus, energy dosage, and scan speed of the laser beam are programmable. Features in the lower layer are offset from features in the upper layer such that these features do not overlap along a plane parallel to a path of the laser beam. Each of the stacked layers includes active devices, such as transistors. Also, the first and second layers may be annealed simultaneously.