Additive nanofabrication by two-photon polymerization (TPP) has recently drawn increased attention due to its sub-100 nm resolution and truly three-dimensional (3D) structuring capability. However, besides additive processes, subtractive process is also demanded for many 3D fabrications. Method possessing both additive and subtractive fabrication capabilities was rarely reported. In this study, we developed a complementary 3D micro/nano-fabrication process by integrating both additive two-photon polymerization (TPP) and subtractive multi-photon ablation (MPA) into a single platform of femtosecond-laser direct writing process. Functional device structures were successfully fabricated including: polymer fiber Bragg gratings containing periodic holes of 500-nm diameter and 3D micro-fluidic systems containing arrays of channels of 1-µm diameter. The integration of TPP and MPA processes enhances the nanofabrication efficiency and enables the fabrication of complex 3D micro/nano-structures that are impractical to produce by either TPP or MPA alone, which is promising for a wide range of applications including integrated optics, metamaterials, MEMS, and micro-fluidics.