The naive response is that you must open each file individually for I/O. By 'tried using open MYDIR "." and foreach to iterate through the files', do you mean you tried something like the following?

#!/user/bin/perl

open (OUTFILE, '>>', 'COID_LIST.txt') or die "Unable to open Write Fil
+e! \n$!";
opendir MYDIR, '.' or die "opendir $dir_name failed";
my @file_list = readdir(MYDIR);
closedir MYDIR, '.' or die "opendir $dir_name failed";

foreach $file (@file_list) {
    open (INFILE, '<', $file) or die "File not found\n$!";

    while (<INFILE>) {
        my $COMPANY_ID = substr $_, 260, 5;
        push @COMPANIES, {comp => $COMPANY_ID};
    }
    close INFILE;
}

foreach (@COMPANIES) {
    $sum{$_->{'comp'}} += $_->{'count'};
    }
#Output in %sum
use Data::Dumper;
print OUTFILE Dumper(\%sum);

close OUTFILE;
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Note that I changed to the three-argument form of open - this is particularly important if your take in a list of files. You should also get into the habit of starting files with use strict;use warnings since it'll save you from typos.