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my $id = '2009-02-12-1234';
my $filename = "file-$id.dat";
...

# it completed ok - upload the completion marker
$ftp->put ( $dummy_file, "$filename.complete" );

foreach my $file (@files) {
 # Only look for the 'upload complete' marker files
...
 # remove the 'complete' marker file
 unlink($file) || die "can't unlink $file - $!"
}