I don't quite understand what you are trying to accomplish, but if it is that you only want the files, with no directory tree in front of them then you need to chdir to the $UploadDir first.

chdir $UploadDir;
$cmd = "tar -cvvf results.tar en_ran.out en-ave.out en_ave_ran.out en_
+ave_ran.out gc-ave.out score_ran.out score-ave_ran.out score-ave.out"
+;
system ($cmd);
[download]