When completing a virus scan of the computer using CA eTrust Vet Anti-Virus the scan log reports that a number of files (58 files to be exact) cannot be scanned, such as NTUSER.DAT, SAM, SECURITY, etc. What files are these, and why can’t they be scanned?

Good work on checking the logs of your virus scanner to ensure that everything is above board. In this case there is nothing to be worried about. All the files which are not being scanned in the list you provided (which has been edited from publication, due to space constraints) are Windows system files that are in-use while Windows is operating. Virus scanners are unable to scan such files because they are in-use and Windows denies access to the files so they cannot be tampered with by malicious programs (e.g. viruses, spyware) due to their highly sensitive nature, such as the SAM and SECURITY files. So, the fact these files will not scan is nothing to worry about.