There are many ways to protect your secret or confidential folders in Windows. You can either lock it with tools like LocK-A-FoLdeR, BuduLock and Freeware Lockbox or hide it using the Windows folder hide option. Another way is to disguise the folders to look like system folders. Disguise Folders is a nice freeware app for Windows which allows you to set your secret folders look like system folders. The app is portable and works with ease. You just need to select the folder to disguise and then select the system folder which you want to be disguised to.
Once you click on the disguise now button, you can see your secret folder turn into a system folder with the same icon as the system folder you have selected. When you try opening the disguised folder, it in fact takes you to the actual system folder and does not open the secret files.
To recover the folder, you can do the same operation, but selecting the folder. The files inside this folder will be safe and will not be deleted or changed.
The app is very handy to quickly disguise your folders without changing any of the settings.