use strict;
use warnings;

my %replace = qw(
    COM  SEC

    MOC  COM
    SEC  COM
    CO   MOC
);
my $searchpat = join '|', sort { length $b <=> length $a } keys %replace;
$searchpat = qr/$searchpat/; # optional, dunno if it speeds up things

my $example = "FOO CO COM BAR MOC SEC";
$example =~ s/($searchpat)/$replace{$1}/g;
print "$example\n";