The correct way to uninstall an OS is always to delete it's partition in Disk Management and then create a new one: Partition or Volume - Delete Partition or Volume - Create New
Are you unable to back up your files you want to save from E so you can delete the old OS partition?
If so you need to mark the partition Inactive, then take ownership of the folders including the Windows Folder that you don't want in order to delete them: Partition - Mark as Inactive - Windows 7 Forums Take Ownership Shortcut
However the Windows folder will fight you, requiring Taking Ownership of sub-folders and individual files, sometimes only possible by permissioning Everyone on the File Properties Security tab. It is an ordeal.
That's why it's easiest to move the data off, delete and re-create the partition and then move data back on, link it to related Libraries in Windows 7: Library - Include a Folder - Windows 7 Forums