Zeolitic Imidazolate Frameworks (ZIFs) based gas separation is proposed to be an energy efficient process compared to conventional processes currently used in the industries. In order to achieve high gas separation factor, diffusion of gases through the size selective aperture of ZIFs has to be maximized suppressing the gas diffusion through the non-selective inter-crystal grain boundary structure. In this regard, a priori depth dependent experimental characterization of pore architecture of ZIF based multilayer membranes is quite essential. In the present study, depth dependent positron annihilation Doppler broadening spectroscopy has been used to investigate the pore interconnectivity and grain boundary structure for alternatively deposited bi- and tri-layers of ZIF-67 and ZIF-8 using fast current driven synthesis method (FCDS). The phase purity and chemical bonding of the films have been established using X-ray diffraction and Fourier transform infra red spectroscopy. The electron microscopy images of the films have shown uniform and densely packed film deposition using the present methodology. The S-E profiles of multilayers films measured using Doppler broadening spectroscopy confirm the modifications in pore interconnectivity and crystal packing as compared to seed films (ZIF-8 and ZIF-67). The S-E profiles of multilayers could not be modeled considering individual ZIF-8 and ZIF-67 films deposited over each other with distinct interface structure. The present study confirms that multilayer deposition of ZIF-8 and ZIF-67 using FCDS leads to modification in crystal packing throughout the bulk of the film. It is confirmed that grain boundary structure is significantly improved in case of multilayers as compared to pure ZIF-67 based film, which can be attributed to the better gas separation performance of multilayers compared to pure ZIF-67 observed in literature.