Bony structures at the skull base were the main obstacle to detection and estimation of arterial stenoses and aneurysms for CT angiography in the brain. Direct subtraction and the matched mask bone elimination (MMBE) have become two standard methods for removing bony structures. However, clinicians regularly find that calcified plaques at or near the carotid canal cannot be removed satisfactorily by existing methods. The blood-plaque boundary tends to be blurred by subtraction operation while plaque size is constantly overestimated by the bone mask dilation operation in the MMBE approach. In this study, we propose using the level of enhancement to adjust the MMBE bone mask more intelligently on the artery- and tissue-bone/plaque boundaries. The original MMBE method is only applied to the tissue-bone boundary voxels; while the artery-bone/blood-plaque boundary voxels, identified by a higher enhancement level, are processed by direct subtraction instead. A dataset of 6 patients (3 scanned with a regular dose and 3 scanned with a reduced dose) with calcified plaques at or near the skull base is used to examine our new method. Preliminary results indicate that the visualization of intracranial arteries with calcified plaques at the skull base can be improved effectively and efficiently.