Been using this script for many years to do that. Works great. The critical part is where you do a /\cM/ match and then just chop the end of the line twice.

#!/usr//bin/perl -w
use strict;
use Getopt::Long;
use IO::File;
use constant USAGEMSG   => <<USAGE;

Usage:  clean-ctrl-m.pl [file]

Options:
        --file                          File to clean (required)
        --help                          This Help

USAGE

my (
        @dir,
        $fh,
        $tmp_fh,
        $file,
        $help,
        $vers
);
$vers = "1.0";

die USAGEMSG unless GetOptions(
        'file=s'        =>      \$file,
        'help'          =>      \$help
);
if ($help) { print "\nVersion: $vers\n"; die USAGEMSG; }
if (not $file) { die USAGEMSG; }

$fh = new IO::File("$file") or die "File not found: $!\n";
$tmp_fh = IO::File->new_tmpfile;

until ($fh->eof()) {
        my $line = $fh->getline();
        if ($line =~ /\cM/) {
                chop($line);
                chop($line);
        }
        print $tmp_fh "$line\n";
}
$fh->close;
$fh = new IO::File(">$file") or die "File not found: $!\n";
seek($tmp_fh,0,0);
until ($tmp_fh->eof()) {
        my $line = $tmp_fh->getline();
        print $fh $line;
}
$fh->close;
$tmp_fh->close;
exit;
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