In this work, we present a quantitative (statistical) 3D morphological characterization of optical fibers used in electric-field sensing. The characterization technique employs propagation-based x-ray phase-contrast microcomputed tomography (micro-CT). In particular, we investigate specialty optical fibers that contain microstructured holes that are electro-optically modified by thermal poling to induce second-order nonlinear effects (SONE). The efficiency of the SONE is reflected in the characterization parameter, Vπ, which is highly dependent on the dimensions of the fiber. The fiber microstructures must be uniform to support the fabrication of reproducible devices. The results obtained using the micro-CT technique show that uncertainty of ±1.7% arises in the determination of the expected value of the voltage that causes a change in the phase of the electromagnetic wave equal to π rad (Vπ ), demonstrating a great advantage, compared with other techniques e.g. SEM, which would need at least 1000 images of the cross-section of an optical fiber, taken at different points, making the process more expensive and time-consuming.