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You can keep your saved worlds if you plan on reinstalling Minecraft later.   Open your file manager and navigate to /home/username/.minecraft, replacing username with your Linux username. Copy the saves folder to another location. When you reinstall Minecraft, you can copy the folder back. In Ubuntu, you can quickly access the Terminal by pressing Ctrl+Alt+T. rm -vr ~/.minecraft/* and press ↵ Enter. You may be prompted to enter your administrator password. This command will delete all of the Minecraft files on your computer.
Backup your saved games (optional). Open the Terminal. Type .