A File System is a combination of structures, records and tables located in different blocks on the CD, possibly scattered all over the CD/DVD.  
A CD or DVD can contain several different File Systems so that different OS can use the most suitable one.

A File System should not be mistaken for the CD's TOC (Table of Contents).
The CD TOC contains the Session and Track Layout.  It does not contain any File System.
File Systems reside in the User data portion of the CD or DVD and a drive itself does not know how to interpret them.
It's up to the host to interpret a File System.

Examples of CD/DVD File Systems : ISO9660, Joliet, Rock Ridge, CD-i, UDF, ...
Examples of HD or Floppy File Systems (*) : FAT12, FAT16, FAT32, NTFS, ...

(*) FAT16 and FAT32 can also be used on DVD-RAM and BD-RE media.FS