Server defragmentation isn’t a task you can do, or even want to do, every day. It can lead to performance loss during defragmentation, so you may want to use some hints and tips, before you run it on a monday morning at 9:00 AM.
Analyze before defragmenting a volume
• Analyze volumes before defragmenting them. After analyzing a volume, a dialog box tells you the percentage of fragmented files and folders on the volume and recommends whether to defragment the volume. Analyze volumes regularly and defragment them only when Disk Defragmenter recommends it. A good guideline is to analyze volumes at least once a week. If you seldom need to defragment volumes, analyze volumes monthly instead of weekly.
Analyze after large numbers of files are added
• Volumes might become excessively fragmented when users add a large number of files or folders, so be sure to analyze volumes after this happens. Generally, volumes on busy file servers should be defragmented more often than those on single-user workstations.
Ensure that your volume has at least 15% free space
• A volume must have at least 15% free space for Disk Defragmenter to completely and adequately defragment it. Disk Defragmenter uses this space as a sorting area for file fragments. If a volume has less than 15% free space, Disk Defragmenter will only partially defragment it. To increase the free space on a volume, delete unneeded files or move them to another disk.
Defragment during low-usage periods
• Defragment file server volumes during low-volume usage periods to minimize the effect that the defragmentation process has on file server performance. The time that Disk Defragmenter takes to defragment a volume depends on several factors, including the size of the volume, the number of files on the volume, the number of fragmented files, and available system resources.
Defragment after installing software or installing Windows
• Defragment volumes after installing software or after performing an upgrade or clean install of Windows. Volumes often become fragmented after installing software, so running Disk Defragmenter helps to ensure the best file system performance.
Above guidelines are taken from Best practices for Disk Defragmenter, found on the Microsoft site
More useful information may be found in two other articles:
Defragmentation: should I defragment my servers
Defragmentation: defragment servers remotely with wmi