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I tried the solutions mentioned in other threads and could not remove the phpgraphy folder left behind as I didn't have the permissions to modify the files. This was using both Filezilla and the Cpanel filemanager.
Using CPanel (it was stuck on a free webhost account) I chose the Fix File Ownership option which gave the following general information:
This feature is useful when you have any files created by PHP (for example if you installed Joomla or used some file upload script), ownership of these files usually changes to "99" or "nobody" and you are not be able to delete or modify such files by FTP or File Manager, you will get "Permission denied" errors (such files can be deleted by PHP script only).
After running this option to fix my file ownership I was allowed to delete the files using the inbuilt filemanager. Hopefully this might help those with the same problem.