I am sure that a lot of people can offer a better, cleaner and more efficient solution, but a couple of simple loops should do the trick.

open (FILE1, "<$file1");
@lines1 = <FILE1>;
close (FILE1);

open (FILE2, "<$file2");
@lines2 = <FILE1>;
close (FILE1);
open (FILE3, ">$file3");

foreach $line1(@lines1) {
     chomp $line1;
     ($x1,$y1,$z1) = split (/ /,$line1);
     foreach $line2(@lines2) {
          chomp $line2;
          ($x2,$y2,$z2) = split (/ /,$line2);
          print FILE3 $x1 - $x2 . "\n";
     }
}
close (FILE3);
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This code is not tested, and lacks the appropriate my,our... but it should give you a good idea of one method to tackle the problem.

Cameron