The clicking noise is most likely caused by a spring connector that touches the bottom of the body:
from another post:
Since a while now I can hear a metallic ticking clicking sound coming from my new MacBook Pro i5 Unibody. It can be described as a glassy, high-pitched scraping sound. Sometimes, moving the computer or resting your hands or just touching it will cause the noise. Other times, the noise just happens of its own accord.
Because I have a SSD I knew it was not the hard drive I was hearing. I did wonder if I was the only person who had this problem, but I quickly found out there are a bunch of others who also complain about this clicking sound inside their MacBook Pro Unibody. There are even some who had record the sound of it or have made some YouTube video to show how it can be reproduced.
Don’t even try to ask the Apple Genius Bar or the Apple Support Department, they do not even know what you are talking about, stating it is the CD laser head locking sensory system you are hearing.
I had finally found a solution, and fixed the problem of this strange clicking sound in my MacBook Pro. All this thanks to Ten 1 Designer’s blog, the maker of the now famous pogo sketch stylus.
Here’s how to solve the tick-click sound in your MacBook Pro Unibody:
You need to unscrew the back cover of your MacBook Pro and remove a little spring connector that touch (and scrape noisily) the bottom of the metallic casing when the computer heat up.
Ten 1 explain why removing this little connector will solve the problem (and it did) and also why it is not a crucial piece of equipment in your MacBook Pro:
The bottom cover of the MacBook Pro serves as a shield for radiated electromagnetic energy. A great shielding strategy is to find a huge piece of metal, and connect your circuit to that metal wherever possible. The MacBook Pro Unibody enclosure and bottom cover make a terrific shielding system.
One of the connectors in this system touches the bottom plate right in the center where it flexes a lot. When the computer heats up, the metal pins in the connector scrape noisily against the cover and chassis. It makes you want to eat your hands.
By removing the connector (two easy screws!), you remove one of the grounding connections between the unibody enclosure and the bottom cover. Don’t worry: there are plenty of other connections, and they are adequate for the purpose.
Result: Quiet, harmonious environment restored.
Fix the ticking clicking sound in your MacBook Pro Unibody - 6ix Passions