3D tomographic data at various scales has increased in availability due to the wide adoption of MicroCT and FIB-SEM technologies. However, upscaling these observations is very challenging. This study provides a template of an upscaling protocol between FIB-SEM data on a micron sized sample and MicroCT data on the same sample region but at millimeterscale. A Devonian North American shale rock fragment is used in this study. Due to the large scale variations in the pore structure and drastic petrophysical property heterogeneity, shale rocks are very challenging and costly to study as compared to rock samples from conventional reservoirs. Using MicroCT with voxel resolution of tens of microns, we are able to identify different rock heterogeneities. A smaller sample from each distinct heterogeneity region is then digitized using FIB-SEM 3D imaging with voxel resolution of a few nanometers. Stokes flow at pore-scale is used to model the absolute permeability tensor, an intrinsic rock property associated with each rock heterogeneity. Afterwards, multiphase porous medium flow at Darcy-scale is conducted on the MicroCT data, constrained by the permeability tensor and the porosity calculated from FIB-SEM data that correspond to each heterogeneity identified from the MicroCT data previously. This feasibility study provides a framework for modeling a wide range of petrophysical parameters in a heterogeneous region by combining imaging and modeling protocols at different scales.