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

my @array = ("M94202", "M94150", "M94297", "M94150", "M94161", "M94161", "M94162");

my %uniq;
my $z = 1;
for (@array) {
    if (/M/) {
        if (exists $uniq{$_}) {
            $_ = $uniq{$_};
        }
        else {
            $uniq{$_} = $z;
            $_ = $z;
            $z += 2;
        }
    }
}
print Dumper(\@array);

__END__

$VAR1 = [
          1,
          3,
          5,
          3,
          7,
          7,
          9
        ];