Researchers have always been interested in finding new and effective materials for protection against radiation. This experimental study aimed to design and fabricate new types of nano-material and micro-material based shields against the ionizing effect of cone beam computed tomography (CBCT) X-rays. To fabricate a flexible prototype, we added dioctyl phthalate (DOP) oil to emulsion polyvinyl chloride (PVC) powder. The paste was mixed and dispersed. Then, nano- and micro-powders of WO3 and Bi2O3 were added to the paste, with the weight ratio of 20% PVC, 20% DOP, and 60% nano- and micro-metals. Using an ultrasonic mixer, the polymer matrix and metals were mixed and a paste with a thick texture was developed. The resultant paste was poured into glass molds and the molds were then heated in an oven. After cooling, the resultant sheets were selected for further experiments. A CBCT unit and dosimeter were used to evaluate the characterization and X-ray shielding properties of the fabricated prototypes. The half-value layers (HVL) for nano-WO3, micro-WO3, nano-Bi2O3, and micro-Bi2O3 were 0.0390, 0.0524, 0.0351, and 0.0374 cm, respectively. In addition, the linear attenuation coefficient (µ) for these materials were 17.77, 13.20, 19.71, and 18.5 cm−1, respectively. The findings indicate that nano-structured samples are more effective in the attenuation of X-ray energy. The nano-structured WO3 prototype was nearly 34% more efficient in attenuating radiation compared to the micro-structured WO3 prototype. This difference in nano- and micro-structured Bi2O3 prototypes was 6.5%.