To make molecular imaging useful in the clinic, accurate image registration must be done to correlate nano-scale events to macro-scale anatomy. The 3D volumetric image registration technique uses visual and quantitative measures to identify the most homogeneous color distribution on a volumetric anatomical landmark. Four phantom PET/CT images were acquired with 5.0±0.1 mm shift interval. The image registration shift was compared with the positioning shift. An accuracy of 0.1° and 0.1 mm was achieved. Cranial PET/CT images from 39 patients were examined. It was found that the average head motion was 0.5-1° and 1-3 mm, even with a stringent head holder. This small but significant misalignment is beyond the capability of conventional visual-based fusion methods used clinically. The 100 μm accuracy is a step forward to register molecular activities to anatomy for high precision interventions.