A novel fluorophore-spacer-receptor has been designed with hydrazono methyl phenol as the receptor, anthracene as the fluorophore and imine (CQN) groups as the spacer. This newly designed fluorophoric system has a receptor that can bind with ferrites and a fluorophore core that can conjugate non-covalently with multiwalled carbon nanotubes (MWNTs) via pi-pi conjugation. The hybrid nanoparticles were thoroughly characterized using Raman, UV-vis and fluorescence spectroscopy. This unique hybrid is further explored as a novel material to screen electromagnetic (EM) radiation. By precisely localizing these hybrids in a given phase of an immiscible co-continuous blend, unique microstructures can be constructed. Herein, blends of polyvinylidene fluoride (PVDF) and polycarbonate (PC) were chosen as a model system. The hybrid nanoparticles were selectively localized in the PVDF phase owing to its higher polarity and were systematically characterized by electron microscopic and solution-dissolution techniques. The hybrid nanoparticles that were designed to shield from the incident EM radiation resulted in 499.99% attenuation, dominated mostly by absorption. This non-covalent approach of conjugating MWNTs with ferrites, aided by the fluorophoric system, was noted to be a more effective way to improve the properties (both bulk electrical conductivity and structural) than direct physical mixing/covalent conjugation approaches. In order to further enhance the shielding effectiveness (SE), a layer-by-layer architecture was constructed essentially with outer layers containing PC/PVDF blends with a MWNT-ferrite hybrid and the inner layers consisting of PC/PVDF blends with only MWNTs. An ultra-thin shield of 0.90 mm showed 499.9999% attenuation suggesting new pathways for designing lightweight, flexible EMI shielding materials.