As long as all files are in the root, something like this should work:
:local FTPserverAddress "192.168.88.2";
:local FTPuser "myUser";
:local FTPpass "myPass";
:foreach FILE in=[/file find] do={
:local name [/file get $FILE name];
/tool fetch address="$FTPserverAddress" src-path="$name" user="$FTPuser" mode=ftp password="$FTPpass" upload=yes;
}
http://wiki.mikrotik.com/wiki/Manual:To ... h#Examples
As far as I know you cannot create directories on the FTP server, so copying directory structures via push is impossible.