We demonstrate an improved femtosecond laser irradiation followed by chemical etching process to create complex three-dimensional (3D) microchannels with arbitrary length and uniform diameter inside fused silica. A segmented chemical etching method of introducing extra access ports and a secondary power compensation is presented, which enables the fabrication of uniform 3D helical microchannels with length of 1.140 cm and aspect-ratio of 522. Based on this method, a micromixer which consists of a long helical microchannel and a y-tape microchannel was created inside the fused silica. We measured the mixing properties of the micromixer by injecting the phenolphthalein and NaOH solution through the two inlets of the y-tape microchannel. A rapid and efficient mixing was achieved in the 3D micromixer at a low Reynolds number.