To pair your remote with a specific Mac or Apple TV, just hold down the menu and the next (fast forward) buttons for 5 seconds making sure you're within 5 inches of the IR sensor on the device.
You can unpair a remote by going into System Preferences (Apple menu > System Preferences) and click security. From the Security System Preference pane, select the "Unpair" button at the bottom the preference pane.
Lastly, you can disable the use of remotes all together. To do this, head back to the Security System Preference pane and click the check box labeled "Disable remote control infrared receiver." This will keep rogue remotes away from your Mac.
Apple Apple TV 3rd-gen