Nanoimprinting techniques are an attractive solution for next generation lithography methods for several areas including photonic devices. A variety of potential applications have been demonstrated using nanoimprint lithography (NIL) (e.g. SAW devices, vias and contact layers with dual damascene imprinting process, Bragg structures, patterned media) [1,2]. Nanoimprint lithography is considered for bridging the gap from R and D to high volume manufacturing. In addition, it is capable to adapt to the needs of the fragmented and less standardized photonic market easily. In this work UV-NIL has been selected for the fabrication process of 3D-photonic crystals. It has been shown that UVNIL using a multiple layer approach is well suited to fabricate a 3D woodpile photonic crystal. The necessary alignment accuracies below 100nm were achieved using a simple optical method. In order to obtain sufficient alignment of the stacks to each other, a two stage alignment process is performed: at first proximity alignment is done followed by the Moire´ alignment in soft contact with the substrate. Multiple steps of imprinting, etching, Si deposition and chemical mechanical polishing were implemented to create high quality 3D photonic crystals with up to 5 layers. This work has proven the applicability of nanoimprint lithography in a CMOS compatible process on 3D photonic crystals with alignment accuracy down to 100nm. Optimizing the processes will allow scaling up these structures on full wafers while still meeting the requirements of the designated devices.