use autodie;
open my $in1, '<', $file1;
open my $in2, '<', $file2;
open my $out, '>', $file3;

for my $row ( 0..7 ) {
    my $line1 = <$in1>; 
    chomp $line1;
    my @line1 =  split / /, $line1;
    my $line2 = <$in2>; 
    chomp $line2;
    my @line2 = split / /, $line2;
 
    my @out;
    for my $col ( 0..11 ) {
         push @out, $line1[$col] - $line2[$col];
    }
    say { $out } join ' ', @out
}
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Since I want to use $col to index the line component arrays, it needs to be zero based. For symmetry, $row should also be zero-based. Otherwise, I would use 1..8 and 1..12, for clarity.