use strict;
use warnings;
use Data::Dumper;

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

my $input1;
my $input2;

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

my $line;
my @columns;

my $nextUnless = 2; # nr of lines to skip
my $CountLines = 0; # total nr of lines in all files

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

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

print "@files \n"; # for testing; are correct files printed?

## now split and print

my @list;
for my $file (@files) {
    open my $FH, "<", $file or die "Cannot open $file $!"
    while ($line = <$FH>) {
      $CountLines += 1;
      next unless $. > $nextUnless;
      chomp $line;
      $line =~ s/^\s+|\s+$//g;
      push @list, [split/\s+/, $line];
      @columns = split /\s+/, $line;  # this is most probably wrong, may be you need to push a reference, as you did in the previous line
    }
    close $FH;
}
print Dumper \@list; # check that the content of @list is what you expect
# ...