chmod 000 denies read, write, and execute rights for itself, your group, and everyone else.
How are files uploaded to the server? Your FTP program can attach files to me when they are downloaded.
root-, $ rm -rf filename
Edit
Umask . Umask 777 000.
, 777 Umask, : grep 'umask 777' /etc/skel/.bashrc
-, Umask 022. , .
cpanel FTP-, ββ Transmit for Mac Core FTP Pro Windows, SFTP, FTP.