This website has many examples of how to use batch files to manipulate downloaded files in the advanced -> External settings of Core FTP Pro (cmd.exe /c c:\bat\yourbatchfile.bat %1 in the post-download field)
http://www.ericphelps.com/batch/samples/samples.htm
Renaming:
http://www.ericphelps.com/batch/samples/namedate.txt