I have a domain atul.99k.org
I am unable to delete old files (PHP MySQL apps).
Every time I try to delete using gftp or the web based file manager, I get an answer 0 files deleted and the files are still there.
Will be grateful if you could help.

Files or directories? If it's a directory you will have to empty the contents before you can remove it, make sure hidden files are on too so you can find any lurking .htaccess's.

You have to set the permissions to CHMOD 777 including the htacess files, if not youll be unable to delete them. Same happened to me.