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MS-DOS organizes data on the hard disk into a series of clusters (allocation units) and then tracks which files are using which clusters through directory structures and the file allocation tables (FATs). Neither users nor applications need to know exactly where specific data is located on the hard disk. When an application needs a file, it simply asks MS-DOS to get it.

Over time, pieces of files may be spread all over the hard disk. When this occurs, retrieving files requires more time. Defragmenter reorganizes the clusters for faster access. (For example, information is stored at the front of the disk, and parts of files are regrouped together). Defragmenter uses interrupt calls 25H and 26H to move the information stored in one cluster to another, directly updating the FATs and directory structures.

Defragmenter operates at nearly the same level as MS-DOS. However, it still uses MS-DOS and is protected from direct interactions with the following:

• Third-party partitioning utilities that modify or translate disk geometry (such as Disk Manager and SpeedStor)
• DoubleSpace and third-party drive compression utilities