A method is provided for the internal processing of a transparent substrate in preparation for a cleaving step. The substrate is irradiated with a focused laser beam that includes pulses having an energy and pulse duration selected to produce a filament within the substrate. The substrate is translated relative to the laser beam to irradiate the substrate and produce an additional filament at one or more additional locations. The resulting filaments form an array defining an internally scribed path for cleaving the substrate. Laser beam parameters may be varied to adjust the filament length and position, and to optionally introduce V-channels or grooves. The laser pulses may be delivered in a burst train for lowering the energy threshold for filament formation, increasing filament length, thermally annealing of the filament modification zone to minimize collateral damage, and increasing the processing speed compared with the use of low repetition rate lasers.