assign_column_names_to_file( \@options_lines, \%{ $files{'options'}{'c
+olumns'} } );

foreach $key (sort keys $files{'options'}{'columns'}{'config'}->%* ){
    print "columns: $key\n";
}

#############################################################

sub assign_column_names_to_file{ # \@options_lines, $file{'options'}->
+{columns} (hash reference)
    my ($options_lines, $columnhash) = @_; #array ref, hash ref
    # this function populates a reference to a hash which has all the 
+column names, numbers, and states

    my $regex__cfg_names = qr"^(\/\*\+\*\/\s+\/\*\|)(.*)\*\/\r?$";
    my $horizontal_offset = 116; #magic number, could calculate dynami
+cally
    #my $horizontal_offset = 0;
    my @letters = ();
    my @config_names = ();
    my @columns = ();
    my $i = 0;
    my $j = 0;
    my $line;

    foreach $line (@$options_lines) {
        # read config names at top of file into $config_name
        if ($line =~ m/${regex__cfg_names}/) {
            #$horizontal_offset = length($1);
            #print (length($1 . "\n") - 1);
            undef @letters;
            @letters = split (/  ?/, $2);
            for ($i = 0; $i < @letters; $i++) {
                if( $letters[$i] ne " " ){
                    $config_names[$i] .= $letters[$i];
                }
                #print STDERR "\nConfig Name:".$config_names [$i];
            }
        }
    }

    for( $i = 0; $i < @config_names ; $i++){
        if( $config_names[$i] =~ m/.*ooo.*/ ){
            #print "skipping $config_names[$i], column " . ($horizonta
+l_offset + $i * 2) . "\n";
            next;
        } else {
            #print "trying to add $config_names[$i], column " . ($hori
+zontal_offset + $i * 2) . "\n";
            $$columnhash{'config'}{"$config_names[$i]"}{'column number
+'} = $horizontal_offset + $i * 2;
            $$columnhash{'column number'}{$horizontal_offset + $i * 2}
+{'config'} = "$config_names[$i]";

            for( $j = 0; $j < @$options_lines; $j++){            
                if ( (length $$options_lines[$j] > $horizontal_offset 
++ $i * 2 ) && (substr($$options_lines[$j], $horizontal_offset + $i * 
+2, 1) ne " ") ){
                        $$columnhash{'column number'}{$horizontal_offs
+et + $i * 2}{'states'}{$j} = substr($$options_lines[$j], $horizontal_
+offset + $i * 2, 1);
                        #print $columnhash->{'column number'}->{$horiz
+ontal_offset + $i * 2}->{'states'}{$j};
                        $$columnhash{'config'}{"$config_names[$i]"}{'r
+owstates'}{$j} = substr($$options_lines[$j], $horizontal_offset + $i 
+* 2, 1);
                }
            }
        }
    }
#    #foreach $key ( keys $$columnhash{'column number'}{$horizontal_of
+fset + $i * 2}->%*  ){
#    foreach $key (sort keys %{ $$columnhash{'config'} } ){
#        print "$key\n";
#    }

    return 0;
}
[download]

That example is neither short nor complete, so once again I'll have to speculate about what it is you're trying to achieve.

In the following code:

sub f {
    my ($r) = @_;
    $r->{level3} = 1;
}

my $rh;
f($rh->{level1}{level2});
[download]

I'm guessing you'd like it to autovivify all three levels of hash, so that the effect is the same as

rh->{level1}{level2}){level3} = 1;
[download]

If so, that can be achieved with

f(\$rh->{level1}{level2}->%*);
[download]

Dave.

use strict;
use warnings;

my @options_lines = ();

my %files = ();
my $key = "";

open (OPTIONSFILE, "<", ".\\include\\options.h");

while (<OPTIONSFILE>){
    push ( @options_lines,"$_");
}

close (OPTIONSFILE);

assign_column_names_to_file( \@options_lines, \%{ $files{'options'}{'c
+olumns'} } );

foreach $key (sort keys $files{'options'}{'columns'}{'config'}->%* ){
    print "columns: $key\n";
}

print "\nExiting\n";
exit 0;

#############################################################

sub assign_column_names_to_file{ # \@options_lines, $file{'options'}->
+{columns} (hash reference)
    ##rewrite based on difopt
    my ($options_lines, $columnhash) = @_; #array ref, hash ref
    # this function populates a reference to a hash which has all the 
+column names, numbers, and states

    my $regex__cfg_names = qr"^(\/\*\+\*\/\s+\/\*\|)(.*)\*\/\r?$";
    my $horizontal_offset = 116; #magic number, could calculate dynami
+cally
    #my $horizontal_offset = 0;
    my @letters = ();
    my @config_names = ();
    my @columns = ();
    my $i = 0;
    my $j = 0;
    my $line;

    foreach $line (@$options_lines) {
        # read config names at top of file into $config_name
        if ($line =~ m/${regex__cfg_names}/) {
            #$horizontal_offset = length($1);
            #print (length($1 . "\n") - 1);
            undef @letters;
            @letters = split (/  ?/, $2);
#            for ($i = 0; $i <= $#letters; $i++) {
            for ($i = 0; $i < @letters; $i++) {
                if( $letters[$i] ne " " ){
                    $config_names[$i] .= $letters[$i];
                }
                #print STDERR "\nConfig Name:".$config_names [$i];
            }
        }
    }

    for( $i = 0; $i < @config_names ; $i++){
        if( $config_names[$i] =~ m/.*ooo.*/ ){
            next;
        } else {
            $$columnhash{'config'}{"$config_names[$i]"}{'column number
+'} = $horizontal_offset + $i * 2;
            $$columnhash{'column number'}{$horizontal_offset + $i * 2}
+{'config'} = "$config_names[$i]";

            for( $j = 0; $j < @$options_lines; $j++){            
                if ( (length $$options_lines[$j] > $horizontal_offset 
++ $i * 2 ) && (substr($$options_lines[$j], $horizontal_offset + $i * 
+2, 1) ne " ") ){
                        $$columnhash{'column number'}{$horizontal_offs
+et + $i * 2}{'states'}{$j} = substr($$options_lines[$j], $horizontal_
+offset + $i * 2, 1);
                        $$columnhash{'config'}{"$config_names[$i]"}{'r
+owstates'}{$j} = substr($$options_lines[$j], $horizontal_offset + $i 
+* 2, 1);
                }
            }
        }
    }
    foreach $key ( keys $$columnhash{'column number'}->%*  ){
    #foreach $key (sort keys %{ $$columnhash{'config'} } ){
        print "$key\n";
    }
    return 0;
}
[download]

This is literally the entire code. Not sure what more you were expecting. I have left in accessing inside and outside the sub to demonstrate the inconsistent syntax. Particularly inside the function, the new syntax is not helpful, and is more than confusing because I have to pay attention to the front and back of hashes.

Additionally, in upper function, I must use \%{} if I want to pass the hash reference - and it must be bracketed because of precedence compared to the first $.