In this study, we propose a drop-out mechanism based on the enhanced interaction between a defect waveguide and defect microcavities in three-dimensional chirped woodpile photonic crystals (WPCs). We first show that light can be gradually slowed down in the defect waveguide (WG), which is obtained by gradually changing the period of the surrounding WPC along the propagation direction. In result, the waveguide mode gradually approaches the band edge region, while this phenomenon has three consequences. First, the Fourier components of propagating wave will be spatially separated as each frequency will reach its zero velocity at different positions. Second, as the wave slows down, it will penetrate deeper into the surrounding cladding, thus increasing the coupling efficiency between the WG and a nearby placed resonator. Third, the high density of states near the band edge result in highly efficient light scattering of a nearby placed resonator, which in turn increases the quality factor of the interaction. Following this idea, the acceptor type cavities, which are tuned to the localized frequencies, are side-coupled to the WG at respective wave localization areas. Furthermore, drop channels have been introduced to read-out the trapped spectra, showing that the targeted frequencies can be detected selectively. Compared to previous studies, our approach has the advantages of low radiation losses, the absence of any reflection feedback and both enhanced quality factor and transmission of the captured light.