If you are formatted NTFS, it is a File based file system there is a Master File Table, a list of all files on the drive and which address or addresses each file occupies. There is a table of contents (The File Allocation Table) listing all available addresses and which file or fragment is saved at that location. If you are formatted FAT32 you have an address based file system. This to some extent depends on your file system format.
This is a simplified overview and not precisely technically correct but aimed at allowing you to visualize and understand what is going on.
First off lets get a general understanding of defrag what it does and how.
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