We present a numerical model of internal modification in bulk borosilicate glass by high repetition rate picosecond laser pulses. We study free-electron dynamics, nonlinear energy deposition and thermal conduction. The optical absorptivity and modification regions both have good agreements with the experimental results. The smooth outer zone is the molten region and the inner-structure formation is caused by high-density free-electrons generated by thermal ionization. Excitation, relaxation and accumulation of free-electron density in the focal volume are analyzed using different pulse shapes and a double-pulse train. The deposited energy distribution and modification zone are controlled by pulse shaping.