I hated having the folders show up twice in my sidebar in the navigation window in Windows 8.1/10, but I love having the sidebar! Once you clean it up, and I add lots of shortcuts to common folders, it really helps speed things up.
Note: This does not remove the actual folders, just the Shortcuts!
To Remove from Windows 8.1 download this Registry-Keys.zip. It has both remove and restore .reg files.
Taken from HowToGeek 8.1.