Why not you hide the Folder and sub folders from option of Folder and Search Option
1. First select the folder which you want to Hide
2. Right click on the Selected Folder
3. Select Properties
4. In the General Option you can find the Hide and Read only Access
Now your folder is in Hidden Mode
When you want to See the Folder and access the Files then you have to set the option to View the Hidden Files in Organize - > Files and Folder Search - > View - >Hidden Files and Folders - > Show Hidden Files, Folders and Drivers