Open the directory containing the files using netrw:
:e ftp://user@website.com/dir/<CR>
Note the trailing slash is important.
Now select all the files you're interested in, using a glob:
mr
*.php<CR>
This will mark all the files matching the pattern. Now you can add them to the arglist and work on them with argdo
:
me
Press <F1>
while in the netrw directory listing for help with the commands available.