Whenever you use system, it's a good idea to test your code with "print" first, so you can make sure you're about to execute the right thing.

Also, you should use system OR ``, but not both.

Once you've decided whether you want system or `` (hint, you want system :), since you don't care about the returned text), you should fix try this:

#!/usr/bin/perl

open(GG,"getall.txt");
                                                            
$dest="/home/test/files/";
$targ="/home/new/newfiles/";
                                     
while ($_=<GG>){
        chomp; # thanks Enlil!
        ($first,$second,$third)=split(/\./,$_);
        print "first: $first second: $second third: $third \n";

        print "cp ${dest}$_ $targ\n";
        #system("cp ${dest}$_ $targ");
}
close(GG);
[download]

Once you're convinced that this does the right thing, comment out the print and use the system line...
--
Mike

(Edit: Thanks, Enlil, for reminding me about chomp.)