Create a batchfile called clean.cmd on your desktop. Fill it with the following content:
Rundll32.exe advapi32.dll,ProcessIdleTasks defrag -b %SystemDrive%
Run that batchfile as admin. Then wait. It’ll take a while.
I typically use this on non-ssd based machines of friends after a clean setup and all the updates. First, I run disk cleaner to cleanup all old updates/upgrades (for machines that i upgrade to win10, for example), then as a last task, i run this command.