The clerk’s office is the courthouse’s central nervous system. (Some courthouses have separate clerk offices for criminal and civil cases.) At a clerk's office, documents relating to all the cases in the court are filed and stored. The courthouse clerk’s office may also issue subpoenas (orders to appear in court), collect fines, and manage other administrative details.
Courthouse clerks also work with clerks assigned to individual courtrooms (often called courtroom clerks). The latter are critical to the day-to-day operation of judges’ caseloads.
For information on related topic, see How do I know where to go once I get to court?