Polarization plays crucial role in light-matter interactions; hence its overall manipulation is an essential key to unlock the versatility of light manufacturing, especially in femtosecond laser direct writing. Existing polarization-shaping techniques, however, only focus on the manipulation in transverse plane of a light beam, namely a two-dimensional control. In this paper, we propose a novel passive strategy that exploits a class of femtosecond laser written space varying birefringent elements, to shape the polarization state along the optical path. As a demonstration, we generate a three-dimensional structured Bessel beam whose linear polarization state is slowly evolving along the focus (typ. 90 degrees within 60 lightwave periods). Such a "helical polarized" Bessel beam allows imprinting "twisted nanogratings" in SiO2 resulting in an extrinsic optical chirality at a micrometric scale, which owns a high optical rotation. Our work brings new perspectives for three-dimensional polarization manipulations and would find applications in structured light, light-matter interaction and chiral device fabrication.