dot files in php directories

When reloading php software to new directories deleting the old dir is often difficult because there is a dot file (often with a majic quotes directrive) so directories aren't empty. I have to telnet to my main account and use command line ftp to delete the (still invisible) offending dot files. Then I can delete the dir with my standard ftp client. I know that I have seen unix systems where I can view/delete dot files with an ftp client. Is that under my control (I have user unix access) or system only control? It's linux/apache.