The answer is in tar, not perl. One of the following lines will do what you want: using tar's -C (change directory) option:

$cmd = "tar vvcCf $UploadDir $UploadDir/results.tar en_ran.out en-ave.
+out ...";
[download]

or using shell tricks:

$cmd = "cd $UploadDir && tar vvcf results.tar en_ran.out en-ave.out ..
+.";
[download]