Defraggler is a free Disk defragmentation software that lets you quickly defrag the individual files you want to, without having to process the whole drive. The new version now lets you even defrag system files at boot-time.
Defraggler for Windows PC
This compact and portable Windows application support NTFS and FAT32 file systems.
Defraggler pushes the capabilities of Defraggler far beyond any other free defragmentation tool, by offering complete offline defrag during the boot process with full OS support.
Additionally, the UI has been improved with a new Drive Map and customizations. They have also re-architectured the internal defrag processes to make it faster and more efficient!
You can now also defrag system files at boot-time.
To do so, open Settings > Options > Defrag tab > Check run boot-time defrag of system files.
You can download it from its home page.
You might also want to check out some of the best free defragmentation software.