Upon initializing NTFS on a disk, 11 metadata files are created in which NTFS stores data associated with disk management. Don't try to delete them. They are the heart of NTFS. (actually I don't think you can). In any case, should you find them, they are not the odd remains of the latest virus or trojan. Metadata files are typically invisible but you can see them by typing

dir /ah metadatafilename

For example, dir /ah $mft

The metadata files and description:

$MFT - Master File Table
$MFTMIRR - Copy of the first 16 records of the MFT
$LOGFILE - Transactional logging file
$VOLUME - Volume serial number, creation time, and dirty flag
$ATTRDEF - Attribute definitions
. - Root directory of the disk
$BITMAP - Contains drive's cluster map (in-use vs. free)
$BOOT - Boot record of the drive
$BADCLUS - Lists bad clusters on the drive
$QUOTA - Contains user quota information (implemented in W2k as $Secure)
$UPCASE - Maps lowercase characters to their uppercase version

NTFS Tips:

Managing Shared Resources and Resource Security
Choosing Between FAT and NTFS
Web versus NTFS Permissions
NTFS Security, Part 2: Implementing NTFS Special Permissions on Your Web Site
Getting the Most from IIS Security
NTFS Permissions
Cancel an NTFS conversion
NT equivalents of NetWare Rights
Access NTFS from DOS, Win95 or Win98 using NTFSDOS driver
NTFS Last Access TimeStamp
xcopy - keep attributes
How To Remove Files with Reserved Names such as LPT1 or PRN
NTFS Metadata files
Disable NTs 8.3 aliases for LFNs under NTFS
Streams displays which NTFS files have alternate streams content
VolumeID changes NT and FAT volume IDs
Create a NTFS partition over 4GB during installation
Windows NT NTFS Directory Compression