Unlike FAT, which has a separate allocation table at the start of a volume, NTFS organizes its centerpiece - the Master File Table (NFT) - with hidden files. The MFT manages all of a volume's files and so-called metadata in a relational database structure. Information on files is arranged into lines; their attributes (hidden, encrypted, compressed, system, etc.) into columns. Metadata containing information on the MFT itself is stored in the first 16 records, totaling 16 kB.

The table for the MFT below shows the first few records. The next MFT data records contain information on the position in the MFT, contents and unused storage space. By the way, files of up to 900 Bytes can fit entirely into one record. For bigger files, the MFT contains pointers indicating where to find them in the memory. The same applies to folders: if they're small enough, they are included completely in the MFT. NTFS manages larger folders whose data structures point to external clusters in a so-called B-tree structure. The advantage of the B-tree structure is that NTFS indexes similar files or their names and thus speeds up searches for specific files.