Not sure if there is a more efficient way of doing it, first click view>show items from subcollections. Now click My library in the navigation pane. This will make it so that all your items in your library appear under "My library"

Then select main window and use the keyboard short cut ctrl+a. This will select all items. Finally, right click and "Move item to bin". This will delete all the items in your library.

I'm not sure there is a way of deleting all your folders in one go - I can't seem to find a way to select them all at once.

@hedwigeisenbarth: For managing a library that size, you really want to use the desktop app.

If you haven't yet synced, you can use Replace Online Library from the Sync → Reset pane of the Zotero preferences without needing to download your entire library first.

Your library is empty. It was probably still syncing.