You can exclude files and folders from your website(FTP/SFTP) backups. The exclude path must be relative to your backup directory.
For example if your backup directory is: /home/demo/public_html/wordpress
Then you can use the following excludes.
|Exclude all files ending with .php||*.php|
|Exclude plugins folder||wp-content/plugins|
|Exclude all cache folders under all subdirectories||cache|