use warnings;
use strict;
use Digest::MD5;

my $file = "$ARGV[0]";
open (my $fh, '<', $file) or die "Can't open '$file': $!";
binmode ($fh);

my $md5 = Digest::MD5->new->addfile($fh)->hexdigest;

print "\n", $file, "\n", $md5, "\n";

my @array = ('d41d8cd98f00b204e9800998ecf8427e', 'd6721344ed0cdc2e8a05
+4a68b7ebc365', 'cee8eb94fd83f8d534bc44bf136ebaa0');
    if( $md5 ~~ @array ) {
        print "The MD5's match perfectly\n";
} else {
    print "The MD5's do NOT match\n";
}
system ( 'pause' );
[download]

Why not just use a hash as a simple lookup table?

This refactored version of your script prints a tab-separated list of all the files specified as arguments on the command line. The report includes a Boolean column indicating if each file's MD5 digest matches one of the digests in the lookup table:  Yes or No.

#!perl

use strict;
use warnings;
use autodie qw( open close );
use Digest::MD5;
use English qw( -no_match_vars );
use File::Glob qw( bsd_glob );

@ARGV or die "Usage: perl $PROGRAM_NAME file ...\n";

@ARGV = map { bsd_glob($ARG) } @ARGV;

local $OUTPUT_FIELD_SEPARATOR  = "\t";
local $OUTPUT_RECORD_SEPARATOR = "\n";

my %md5_digests_table = map { $ARG => 1 } qw(
    d41d8cd98f00b204e9800998ecf8427e
    d6721344ed0cdc2e8a054a68b7ebc365
    cee8eb94fd83f8d534bc44bf136ebaa0
);

for my $file (@ARGV) {
    open my $fh, '<', $file;

    binmode($fh);

    my $md5 = Digest::MD5->new()->addfile($fh)->hexdigest();

    close $fh;

    my $match = exists $md5_digests_table{$md5} ? 'Yes' : 'No';

    print $file, $md5, $match;
}

exit 0;
[download]