An Australian bituminous coal is imaged at high resolution of 16.1 μm with (wet) and without (dry) X-ray attenuating fluids present in the pore space using a large-field three-dimensional microfocus helical X-ray computed tomography (micro-CT) instrument. Scanning Electron Microscope (SEM) is conducted on slices of the specimen to visualize coal micro-features up to resolution of about 15 nm. Two- and three-dimensional image registration techniques are used to precisely overlay micro-CT tomograms of the core plug in dry and wet conditions and SEM images to yield detailed three-dimensional visualizations of the geometry and topology of the fracture systems in coal. SEM images are also used to produce a calibration curve based on the relationship between the micro-CT intensity values and the true apertures of fractures within coal. This eliminates the need for two sets of imaging. Advanced filtering algorithms are applied to segment the micro-CT image into four distinct phases: resolved fractures, sub-resolution pores and fractures, macerals, and minerals. The application of micro-CT in determination of relative age relationships between adjacent geological features is presented. The distribution of resolved aperture size within the coal sample is investigated and the variation of permeability and porosity in several sub-samples of the coal is plotted. The analysis suggests that coal permeability is independent of porosity and is likely affected by other petrophysical properties such as lithotype. To include the effects of mineral phase on coal properties, we remove the segmented mineral phase and merge it to the resolved fracture phase. This analysis affirms that minerals are deposited in highly connected regions.