"Secretary" is not used to refer to office workers any more, at least in the United States. It used to mean someone who handled correspondence for a specific person, but now people have computers to handle much of the work that secretaries used to do. That job is different now, and is called "Administrative Assistant". It consists of many different functions that focus on making sure the boss stays on track.
"Clerk" is a general term referring to a specialized role handling documentation of a certain kind. For example, a bank clerk might file and retrieve financial transactions, while a medical records clerk would file and retrieve patient charts.