The root folder, also called the root directory or sometimes just the root, of a partition or folder is the "highest" directory in the hierarchy. You can also think of it in general as the beginning or start of a particular folder structure.
Create main folder
The root directory contains all the other folders in the drive or folder, and can of course contain files as well. You can visualize this with an inverted tree with the roots (the root folder) at the top and the branches (sub folders) at the bottom; the root is what holds all the lower items together.
For example, the root directory of the main partition on your computer is probably C:/. The root directory of your DVD or CD drive might be D:/. The root of the Windows registry is where hives like HKEY_CLASSES_ROOT are stored.
The term root can also be relative to the location you're talking about. For example, a program that installs in C:/Programs/Example uses that specific folder as its root, with possibly a series of subfolders underneath it.