Minecraft use two different type of file to save your world. Each of these file has a piece of world inside made up by 512 blocks almost. Just imagine your world made up by a huge grid. Each square is a file and the name of the file is decided according to the position. To use the tool you have to browse the folder in which you have these file, usually they are stored in minecraft_folder/saves/worldName/region/r.1.0.mca and this is the file that you have to browse(the extension can be mca or mcr). Then you have to provide 3 different coordinates C1, C2 and C3, corresponding to the region that you would like to save : C1 is the top left angle coordinate, C2 is the top right angle coordinate, C3 is the bottom left angle coordinate. Once this just press "Save chunks" and in your region folder you will see a new folder named Saved; inside this folder you will have the files that you need to keep safe. Once you stored your important files, then these file are the only files that you have to keep in region folder.
That's all! Here the tutorial with the youtube Video!