The femtosecond laser facilitated two-photon polymerisation (2PP) technique is a power fabrication tool for various arbitrary shaped micro-optical devices, among them photonic crystals (PCs) representing a hot topic . Due to their unique optical properties and potential capability to miniaturise optical system, three-dimensional (3D) PCs have attracted much interest in the last two decades. Various fabrication techniques have been proposed and demonstrated. However challenge remains when near-infrared (NIR) or visible PCs compatible with the current telecommunication infrastructure are fabricated because periodicities comparable to the wave-length of illumination light have to be achieved. In this paper, by using the femtosecond laser facilitated 2PP technique, high precision 3D polymer woodpile PCs possessing NIR (∼1.1 μm) bandgaps with nearly 100% suppression in transmission have been achieved. The NIR photonic bandgaps can be continuously tuned to a shorter wavelength region by employing a thermal annealing process, and eventually leads to woodpile PCs having bandgaps at a wavelength shorter than 1 μm. To characterise the 3D PCs and to optimise the fabrication process, near-field optical microscopy has been employed to obtain both the morphology and optical properties of the PCs simultaneously. The experimental results demonstrate that the near-field measurements provide significant additional information about the optical properties of the devices, which has been previously inaccessible .