The CPU beep is a really irritating thing in Linux distros and sometimes the graphical sound manager does not work when shutting it up.
Fortunately there is a simple way to do it in terminal. In Ubuntu (and distros based upon it) type:
gksudo gedit /etc/modprobe.d/blacklist
In Debian type:
And add the following line to the file:
Save it and reboot. Now the CPU beep should be disabled!