Able to precise control and manipulate materials’ states at micro/nano-scale level, femtosecond laser micro/nano processing technology has underwent tremendous development over the past three decades. Free-forming three-dimensional microscale functional devices and inducing fascinating and unique physical or chemical phenomena have granted this technology with powerful versatility that no other technology can match. As this technology advances rapidly in various fields of application, some key challenges have emerged and remain to be urgently addressed. This review firstly introduces the fundamental principles for understanding how femtosecond laser pulses interact with materials and the associated unique phenomena in section 2. Then micro/nano-fabrication in transparent materials by femtosecond laser processing is presented in section 3. Thereafter, several high efficiency/throughput fabrication methods as well as pulse-shaping techniques are listed in section 4, and section 5 reviews four-dimensional and nanoscale printing realized by femtosecond laser processing technology. A special attention is paid to the heterogeneous integration of functional materials enabled by femtosecond laser processing in section 6. Several intriguing examples of three-dimensional functional micro-devices created by femtosecond laser based manufacturing methods such as microfluidics, lab-on-chip, micro-optics, micro-mechanics, micro-electronics, micro-bots and microbiodevices are reviewed in section 7. Finally, a summary of the review and a perspective are proposed to explore the challenges and future opportunities for further betterment of femtosecond laser micro/nano processing technology.