A typical Linux system has the following top level directories:
bin dev home lost+found opt root sys usr
boot etc lib mnt proc sbin tmp var
This is a well thought out structure that divides data by type and importance to running your computer. Bin, sbin and usr contain binary files of decreasing criticality. Etc contains configuration information for your programs. Var contains logs and other temporary files.
The files are referred to like web pages are.
/ is the top level directory, called "root"
/usr is the root directory "usr"
/usr/X11 is the X11 sub directory of usr
/usr/X11/XF86Config-4 is a file located in the previous directory.
Linux does not use three letter extensions in a functional way, though programs can and extensions they can be used for readability. Some shells color code different files on listing for further readability.