grep command - help!

I have recently started using SmartFTP to get data off a Unix machine. We used to identify which file we wanted by using the unix 'grep' command. We don't see any way of using grep in SmartFTP. Is it possible or is their an alternative way.

Typically we'd put grep 123456789 * once in the relevant directory and it would return all files will the 123456789 in them.

You cannot execute Unix commands over an FTP connection. You should either connect via SSH, grep the files, move matches to a separate directory, and download that directory in SmartFTP. Or you could try to use exclusion filters (in the Settings under Transfer -> Filters), which will be quite hard in your case I guess. What you would need are inclusion filters.