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A new microchannel fabrication technology for fused silica substrate is presented. A mode-locked laser was used to fabricate straight microchannels in a fused silica substrate by laser plasma-induced plasma. The depth of the channels is up to 5 mm and there are no thermal cracks around the channel. We studied the ionization mechanism of optical breakdown formed by laser pulses and discussed the optical breakdown threshold. A mechanism is proposed to explain the formation of the microchannels and the characteristics of the microchannels are analyzed through the laser pulse characteristics.