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The utility that is used to realign the file structure on a disk for optimization is the disk defragmenter, commonly referred to as "Defrag." This tool organizes fragmented data on a disk, which can improve file access times and enhance overall system performance. When files are created, deleted, and modified over time, they can become fragmented, meaning that they are not stored in contiguous spaces. Defrag consolidates these fragments, arranging files in a more efficient manner so that the read/write heads of the hard drive have to move less to access the data.

The other utilities mentioned serve different purposes: Disk Cleanup is used to free up disk space by removing unnecessary files, Disk Manager is a tool for managing disk partitions and volumes, and System Restore helps users revert their system files and settings to an earlier point in time. While they contribute to system maintenance and management, they do not specifically address file fragmentation or disk optimization. Thus, Defrag is the appropriate choice for optimizing the file structure on a disk.