You can't edit an existing file like that, use separate file handles for read/write

#!perl
use strict;
use warnings;

my $libFile = 'testfile';
my $filename = $libFile.'.html';
my $remove   = '<div><div class="blue"><\/div><\/div>';

open my $in, '<', $filename or die "Failed to read '$filename': $!";
my @array = <$in>;
close $in;
    
my $matchspotter = 0;    
for ( @array ) {
  if ( s/$remove//g ) {
    ++$matchspotter;
  }
}
print "\n$matchspotter lines replaced";

$filename  = $libFile.'_chg.html';
open my $out, '>', $filename or die "Failed to write '$filename': $!";
print $out $_ for @array;
close $out;
[download]