Femtosecond laser two-photon (multi-photon) micro/nano-processing technology gets the extensive and in-depth research, and is more specifically applied in many frontier fields because of its excellent designable three-dimensional (3D) processing capacity, high spatial resolution, and low additional damage. In this review, we introduce the latest concrete applications and progress of femtosecond laser direct writing (fsLDW) technology in diverse fields with various materials, emphatically, the related work on biological materials′ fsLDW processing. Especially, by combining with the advanced fsLDW technology, protein-based materials have been studied and explored in various functional bio-related micro/nano-devices and systems based on their unique physical, chemical, and biological characteristics.