Disclosed herein are methods for laser welding together layers of transparent polymeric materials by first making high-contrast marks in transparent polymeric materials using femtosecond, picosecond or nanosecond pulsed fiber lasers and then creating localized welds at the areas of the high-contrast marks. Such welds can be formed in multiple layers of transparent polymeric materials. Systems for making welds and parts welded together according to the methods also disclosed.