Methods and systems for three dimensional large area welding and sealing of optically transparent materials are disclosed, including generating a beam of ultra-short pulses from an ultra-short pulsed laser; directing the beam to an acoustic-optic modulator to control the repetition rate of the beam; directing the beam to an attenuator after passing through the acoustic-optic modulator to control the energy of the beam; directing the beam to a focusing lens after passing through the attenuator to focus the beam between a top substrate and a bottom substrate in order to weld the top substrate to the bottom substrate, wherein the top substrate and the bottom substrate are in intimate contact; and controlling the position of the top substrate and the bottom substrate relative to the beam using a three-axis stage in order to weld the top substrate to the bottom substrate at different points. Other embodiments are described and claimed.