Open up the terminal and enter;
$ sudo gedit /etc/modprobe.d/blacklist
add the following line at the bottom of the file;
#Annoying speaker beep
blacklist pcspkr
then save and reboot your pc and the beeps have gone :)
Alternatively if you dont want to reboot you can execute the following command in the terminal;
$ sudo rmmod pcspkr
and your done, no more annoying beep but if you do want the beep back again for some reason then just remove the line
#Annoying speaker beep
blacklist pcspkr
from your /etc/modprobe.d/blacklist file :/