Yes you can manipulate the files/folders using Helm.
Use the following steps.
1) Loging on Helm CP
2) Click On Domain Option.
3) Select a particular Domian in which you want to change the files/folder
4) Click on File Manger.
5) In File Manager you can view all of your files/folders.
6) You can use various option for manipulating the files/folder like delete the file/folder,create the files/folder etc.