If he finds a pen on the desk and does not know who its owner is, what should he do with it?

Praise be to Allah.

If an employee or student finds a pen or tool on his desk that does not belong to the company he is working for, then it probably belongs to one of his friends or clients, so he has to tell them about it and give it back to its owner. If no one recognises it, or there are no other employees except him, then it is lost property, which is subject to further discussion: 

If it is of little value it is permissible to take it and make use of it, and he does not have to announce it, such as if the pen is not worth more than 50 riyals or so. 

If the lost property is of considerable value in people's eyes, then he has to announce it for a year before keeping it. 

For the rulings on lost property, please see the answer to question number 5049. 

And Allaah knows best.