Generally, most the registry entries of USB devices can be found at the following registry keys:

System\controlset\
CurrentControlSet\Control\DeviceContainers
CurrentControlSet\Control\DeviceClasses
Software\Microsoft\Windows\Shell\MuiCache
All these traces pile up, and even registry cleaners may miss them.

USBOblivion is portable freeware that lets you erase all the traces of USB-connected drives and CD-ROMs from the Windows registry. To analyze the used USB devices and CD-ROM entries in your PC, make sure that the Do real clean box is unchecked. This will only scan your computer and list the entries.

usboblivion

Once you are sure that you want to clean the traces, check the ‘Do real clean’ box and click on Clean. By default, this software lets you save backup .reg file. This is good, as before removing the traces from the registry, they get backed up in the form of a .reg file, which is saved in the user’s Documents folder. Once you feel that you should restore these registry entries in your PC, by double-clicking on the backup.reg you can import in the registry editor. You can also use Regbak freeware to create a backup of the registry files and restore back.

USB Oblivion is compatible with Windows XP, Windows 2003, Windows Vista, Windows 7, Windows 8, both 32-bit and 64-bit versions. You can download it from here.

You might be interested in USBDeview also, which is similar in function to USBOblivion.

If you have problems with your USB device, you can troubleshoot using Microsoft Windows USB Troubleshooter. It works well with Windows 7, 8,8.1 and Win 10.

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