The hard disk itself reads and writes 512 byte sectors - just like Compact Flash and MMC cards. Formatting (on a PC) reads all the sectors, locks out the bad ones and creates the file system. The file system is really just data structures to store the required information to locate where the particular files are stored.

If you were doing a data logger and only needed to log one data file as fast as possible - you would just write the data to sequential sectors - no file system needed. But if you wanted to do a MP3 player and you wanted many files - then you might want some sort of file system. One of these is the Microsoft FAT filesystem which the PC can read directly.

There are other threads that discuss this in more detail and have links to the microsoft documentation that explains the FAT filesystem.