How to clear Ubuntu notifications?

Kill the notify-osd program. That'll stop it from notifying until you reboot.

The package responsible for displaying the notifications is notify-osd . You can remove it by opening up a terminal and running the following command:

sudo apt-get remove notify-osd

Fair warning: this will permanently disable all notifications.

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If you later decide you want the notifications back, you can run the following command:

sudo apt-get install notify-osd

In Ubuntu 12.04, you can use NotifyOSDconfig as explained here:

sudo add-apt-repository ppa:leolik/leolik
sudo add-apt-repository ppa:amandeepgrewal/notifyosdconfig
sudo apt-get update
sudo apt-get install notifyosdconfig

Then you can run the program "NotifyOSD Configuration" from Dash Home. Select the option "Close Bubble on Click" and you are done :)