The filesystem is divided into many parts; usually along the lines of a root filesystem with /bin, /lib, /etc, /dev, and a few others; a /usr filesystem with programs and unchanging data; a /var filesystem with changing data (such as log files); and a /home filesystem for everyone's personal files. Depending on the hardware configuration and the decisions of the system administrator, the division can be different; it can even be all in one filesystem.
Chapter 5 describes the filesystem layout in some detail; the Linux Filesystem Standard covers it in somewhat more detail.