As suggested above, you want to use a hash-of-arrays (HoA) to store the "sub-*" records from the second flat file, keyed by company name. It would also be useful for the strings from the first flat file to be stored in a simple hash as well (as you read from that file), again keyed by company name. So, somthing like this to read the two files:

my %f1hash;
my %f2hash;

my $f1 = "company_file.dat";
my $f2 = "other_file.dat";

open( F, $f1 ) or die "can't open $f1: $!";
while (<F>) {
    chomp;
    my ( $co, $url, $dir ) = split /\|/;
    $f1hash{$co} = "$co, $url, $dir<BR>\n";
}
close F;
open( F, $f2 ) or die "can't open $f2: $!";
while (<F>) {
    chomp;
    my ( $co, $url, $dir, $mdir ) = split /, */;
    push( @{$f2hash{$co}}, "  -$co $url $dir<BR>\n";
    warn "$f2 contains $co, not found in $f1\n" unless exists( $f1hash
+{$co} );
}
close F;
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Then when you're printing stuff out, do something like this:

for (sort keys %f1hash) {
    print $f1hash{$_};
    print @{$f2hash{$_}};
}
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