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Why some empty folders can't be deleted ?

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Depending on the applications, they may have had drivers or something that loads and starts with the core of the OS, and the folders are referenced by these. Or active parts of the app were never removed from RAM. Rebooting should help.

It may be that the apps didn't uninstall properly (bad design, or the OS is "confused"). It might help to run a gentle registry cleaner (like the registry cleaning function of CCleaner) to remove straggling registry references to these folders.

Some applications, for example, some versions of Norton internet security apps, require going to the vendors site to get a purpose-built "cleanup uninstaller" to truly remove the app.

If none of this is helping you, please let us know what operating system you are using, what uninstalled applications are involved, and which folders refuse to go away.