Your requirements:

I need to take the first x co-ord in file 1, and substract the x value in file 2 from it - repeat for all x values in file 2.

My code:

use strict;
use warnings;
$|++;

use constant X => 0;
use constant Y => 1;
use constant Z => 2;

# take the first x co-ord in file 1
my @f1_coords = do {
    my $filename = 'file1';
    open( my $fh, "<$filename" )
        or die "Cannot open '$filename' for reading: $!\n";
    my $line = <$fh>;
    close $fh;
    split( ' ', $line );
};

# substract the x value in file 2 from it - repeat for all x values in
+ file 2
my $filename = 'file2';
open( my $fh, "<$filename" )
    or die "Cannot open '$filename' for reading: $!\n";

my $outname = 'file3';
open( my $out_fh = ">$outname" )
    or die "Cannot open '$outname' for writing: $!\n";

while (my $line = <$fh>)
{
    my @f2_coords = split( ' ', $line );

    print $out_fh $f1_coords[X] - $f2_coords[X], $/;
}

close $out_fh;
close $fh;
[download]

You will want to read through my code a few times. It contains a ton of Perl idioms that may help you learn your way. Enjoy!