We report a novel 3D NanoImprint methodology with very high vertical resolution well below 1nm and a minimum surface roughness down to 0.2nm in root mean square (rms) which is attractive for several applications. We introduce our 3D NanoImprint methodology in fabricating 3D filter cavities of Fabry-Perot filter arrays for optical nanospectrometers. A large number of different cavity heights can be fabricated in one single imprint step using this high resolution, low-cost 3D NanoImprint technology. The key issue of developing 3D NanoImprint technology is the fabrication of high resolution templates. The novel 3D templates contain arrays of negative or positive checkerboard-like mesa structures with currently up to 64 different heights. Different types of 3D templates were developed and adapted to cutting edge NanoImprint methods and imprint resists. The performance of different 3D NanoImprint recipes was investigated. Based on the novel 3D NanoImprint technology developed in this work, static Fabry-Perot filter arrays with NanoImprinted cavities indicated rather high filter transmission (best single filter >90%), small line widths (about 2nm in full width at half maximum) and broad stop bands.