Whenever you type in a command your shell searches your PATH variable to check which directories to search for the command in. You can see your path by typing 'echo $PATH'. If you had your path set to every directory on the machine it would take forever to find and execute the command you typed.
Linux does organize similar files in directories though. Binary executable files are usuall in bin or sbin directories and these directories are sometimes in your path. Directories like /usr/bin, /usr/local/bin are usually in your path. However, it is not always the case that all binary executables are in bin directories therefore sometimes you must either put pathnames or cd to the direcotory where you want to execute commands.
If you want to search for a particular command or file you can use the find command:
find . -name filename
Hope this helps.