Femtosecond laser micromachining has been widely used in laser material processing because of its unique advantages of low thermal effects, high precision and three-dimensional processing capability inside materials. The recent advances of the application of femtosecond laser microfabrication combined with femtosecond laser pulse shaping to micro-nanofabrication in transparent materials are reviewed. These techniques possess an important application prospect in novel integrated optics and micro- and nano-optics.