The files on a hard disk are usually organized into directories or folders. Choosing a suitable folder for storing one's files and finding the files again are tasks that cause more problems than most software designers realize.
Many users can't overview the directory structure. When they store a file, they have no idea afterwards which directory they have put their file into. Obviously, they have big problems finding their files again when they need them. I have often seen experienced users storing all their data files in the root of the hard disk, on the desktop, or together with the program files.
Any software that allows the user to store files should encourage the user to store their files in a suitable place. One solution is to create a directory for data files belonging to the program in question and show this directory as the default the first time the user gets a "Save as" dialog box.
The procedures for storing files should of course be the same for all programs running under the same operating system. Don't invent your own file management system - use the standard dialog boxes provided by the operating system.