Microporous carbonates host a significant portion of the remaining oil-in-place in the giant carbonate reservoirs of the Middle East. Improved understanding of petrophysical and multi-phase flow properties at the pore-scale is essential for the development of better oil recovery processes. These properties strongly depend on the 3D geometry and connectivity of the pore space. In this study, we harnessed the unique capabilities of fluorescence confocal laser scanning microscopy (CLSM) to capture both macroporosity and microporosity, down to 0.1 µm, to provide a more representative 3D representation of pore space compared to traditional methods. The experimental procedure developed was specifically designed to enable highresolution confocal 3D imaging of the pore space of carbonate systems. The protocol aims to render carbonates more "transparent" to CLSM by imaging etched epoxy pore casts of the sample and minimizing CLSM signal scattering. The resulting highquality 3D images of the multi-scale pore space allow more reliable petrophysical interpretation and prediction of transport properties. Additionally, we present a robust pore imaging approach that correlates 2D images produced by scanning electron microscopy (SEM) with the 3D models produced by CLSM that cover a range of scales, from millimeters in 3D to micrometers in 2D. For the first time, multi-color fluorescence confocal imaging was employed to characterize the geometric attributes of a porous medium. We foresee that the protocol developed in this study could be used as a standard protocol for obtaining high-quality 3D images of epoxy pore casts using confocal microscopy, and could contribute to improved characterization of micritic carbonate reservoirs and oil recovery methods. We also demonstrate the advantages of multi-scale and multi-color confocal images in realizing more accurate evaluations of petrophysical properties. Finally, we demonstrate that micro 3D printing (two-photon polymerization) can potentially be used to fabricate micromodels with sufficient resolution to capture the geometric attributes of micritic carbonates and that can replicate the inherent 3D interconnectivity between macro- and micro-pores.