With multiple files then maybe what you want is a 3 dimensional array ?

#!/bin/perl/
use strict;
use warnings;

my $molec1 = "molec1";
my $molec2 = "molec2";

my $path = "/store/group/comparisons";
my @matrix;
my @files;

for my $i (1..3){
  push @files, $path."/File-$molec1-cluster$i.out"
}

for my $j (1..2){
  push @files, $path."/File-$molec2-cluster$j.out"
}

my @all = ();
for my $filename (@files){
  open my $fh,'<',$filename or die "Could not open $filename";
  my @matrix = ();
  while (my $line = <$fh>){
    next if ($line  =~ /^#/);
    chomp $line;
    push @matrix,[split /\s+/,$line];
  }
  close $fh;
  push @all,\@matrix;
}

my $matrices = scalar @all;
for my $i (0..$matrices-1){
  print $files[$i]."\n";
  my $rows = scalar @{$all[$i]};
  for my $r (0..$rows-1){
    my $cols = scalar @{$all[$i][$r]};
    for my $c (0..$cols-1){
      print "$all[$i][$r][$c] "
    }
    print "\n";
  }
  print "\n";
}
[download]