I was recently working with SYNC TOYwhere I had Visual Studio files stored in a directory the Visual Studio application created for me when I started the project. I tried to used sync toy, a backup utility also from Microsoft that simply synchronizes or echos files from one directory to another. The problem was I had a project folder with the same name as the subfolder with the same project. SYNC TOY would only dump the contents of the second branch of the tree into the first branch. This made a real mess that I couldn't clean up and I wanted the project to maintain the same file and folder structure as the original project because if things go wrong I want to put it back the way it was before the failure.
I found a free utility that seems to work out well. It creates a full tree and ultimately folders containing files from what ever branch of the tree you select. You can also create backup projects and add the individual backups to a single project to back up with one click. If you want to speed things up and you only have one folder needing backing up then you can run the backup for just that folder.
This is a full featured backup / files sync utility.