For Windows operating system, there is not any difference between the BestCrypt virtual drives and other regular drives in the system. All disk utilities work with the virtual drives in the same way as they work with regular drives. The drive must be formatted using some file system recognized by Windows. Currently there are three file systems supported in Windows 95/98/ME (FAT12, FAT16 and FAT32), three file systems supported in Windows NT (FAT12, FAT16 and NTFS), and four file systems supported in Windows 2000/XP/Vista (FAT12, FAT16, FAT32, and NTFS).
To allow user to choose the file system for BestCrypt virtual drive, use standard Format operation available in the Windows operating system.
When you create new BestCrypt container, you may choose the file system which is the most suitable for your needs. The following table may be helpful here:
| File System | DOS | Windows 95/98/ME | Windows NT/2000/XP/Vista | Comments |
| FAT12 | YES | YES | YES | Windows 95/98/ME uses it automatically if disk size less than 32 Mbytes |
| FAT16 | YES | YES | YES | Windows 95/98/ME uses it automatically if disk size less than 512 Mbytes |
| FAT32 | NO | YES | YES (except NT) | FAT32 uses disk space more efficiently than FAT16 if the disk size is larger than 512 Mbytes (FAT32 is as effective as FAT16 if disk size is more than 256 MB and less than 512 MB.) |
| NTFS | NO | NO | YES | Reliable file system designed specially for Windows NT/2000/XP/Vista |
BestCrypt asks user to choose the file system for new file-container in the following cases: