A practical issue in determining a (U–Th)/He age is the correction factor (F_He) that accounts for potential He loss due to alpha ejection during the decay of U and Th located in the outer 20 µm of a mineral grain. An accurate determination of F_He is affected by the accuracy of measurements made by individual observers and the need for a subjective assessment of crystal morphology relative to an ideal crystal shape. Other issues include the presence of latent mineral inclusions or fracture planes that are potential pathways for helium loss. These issues are potentially most important for detrital grains where grain shape and transparency have been affected by weathering. We used X-ray Micro-Computed Tomography (MicroCT) analysis to objectively and quantitatively address these problems. Using traditional microscopy, four workers with considerable experience in U–Th/He studies independently examined the same set of apatite and zircon grains and reported F_He values that agree to within 4% and 9%, respectively. These same grains were then imaged and measured using MicroCT to obtain X–Y–Z dimension, surface area (S) and volume (V) data. F_He values calculated using the MicroCT S/V differed by up to 24% as compared to microscope-based F_He determinations. The largest discrepancies occurred in small grains with deviations from ideal hexagonal/tetragonal dipyramidal grain morphology. A significant advantage of MicroCT scans is the ability to computationally excise the outer 20 µm layer from the grain via a 3D-erosion procedure. The “effective” F_He is proportional to (eroded V/original V) and objectively accounts for the daughterless parent component in each grain independent of morphology and without the need for microscopic measurements. The “effective” F_He determined by triple erosion is up to 6% smaller than that derived using traditional microscopy methods. MicroCT can also be successfully used prior to analysis to reveal internal fractures, mineral and fluid inclusions to 1 µm resolution via density and elemental contrasts, and to provide accurate volume measurements for the calculation of U and Th concentrations in single grains.