Methods and systems for ultrashort pulse laser processing of optically transparent materials are disclosed. At least one embodiment includes a method for welding materials with ultrashort laser pulses to create a bond through localized heating, at least one material being transparent at a laser wavelength. The ultrashort pulse duration causes nonlinear absorption of the laser radiation, and the high repetition rate of the laser causes pulse-to-pulse accumulation of heat within the materials. The laser is focused near the interface of the materials, generating sufficiently high fluence at the region to be welded. This minimizes damage to the rest of the material and enables fine weld lines. In various implementations the laser is focused near the sub-surface interface between two materials, generating high fluence at the region proximate to the laser focus with minimal modification to the surrounding region, including areas above and below the laser beam waist.