Thanks for the replies! Here is the final code that sets both IE and Firefox proxy settings.

use strict;
use Win32::TieRegistry ( Delimiter=>"/", ArrayValues=>1 );
&setProxy();
###############
sub setProxy{
    #Set access to use proxy server (IE)
    #http://nscsysop.hypermart.net/setproxy.html
    my $server=shift || "localhost";
    my $port=shift || 8080;
    my $enable=shift || 1;
    my $override=shift || "127.0.0.1;<local>";
    #set IE Proxy
    my $rkey=$Registry->{"CUser/Software/Microsoft/Windows/CurrentVers
+ion/Internet Settings"};
    $rkey->SetValue( "ProxyServer"   , "$server\:port"    , "REG_SZ"  
+  );
    $rkey->SetValue( "ProxyEnable"   ,pack("L",$enable)    , "REG_DWOR
+D" );
    $rkey->SetValue( "ProxyOverride" , $override         , "REG_SZ"   
+ );
    #Change prefs.js file for mozilla
    #http://www.mozilla.org/support/firefox/edit
    if(-d "$ENV{APPDATA}\\Mozilla\\Firefox\\Profiles"){
        my $mozdir="$ENV{APPDATA}\\Mozilla\\Firefox\\Profiles";
        opendir(DIR,$mozdir) || return "opendir Error: $!";
        my @pdirs=grep(/\w/,readdir(DIR));
        close(DIR);
        foreach my $pdir (@pdirs){
            next if !-d "$mozdir\\$pdir";
            next if $pdir !~/\.default$/is;
            my @lines=();
            my %Prefs=(
                 "network\.proxy\.http" => "\"$server\"",
                 "network\.proxy\.http_port" => $port,
                 "network\.proxy\.type" => $enable,
                );
            if(open(FH,"$mozdir\\$pdir\\prefs.js")){
                @lines=<FH>;
                close(FH);
                my $cnt=@lines;
                #Remove existing proxy settings
                for(my $x=0;$x<$cnt;$x++){
                    my $line=strip($lines[$x]);
                    next if $line !~/^user_pref/is;
                    foreach my $key (%Prefs){
                        if($line=~/\"$key\"/is){
                            delete($lines[$x]);
                                  }
                             }
                        }
                   }
              if(open(FH,">$mozdir\\$pdir\\prefs.js")){
            binmode(FH);
            #print "Writing $mozdir\\$pdir\\prefs.js\n";
            foreach my $line (@lines){
                $line=strip($line);
                   print FH "$line\r\n";
                  }
            foreach my $key (sort(keys(%Prefs))){
                print FH qq|user_pref("$key",$Prefs{$key});\r\n|;
                }
            close(FH);
            return 1;
            }
              }
         }
    return 0;
    }
###############
sub strip{
    #usage: $str=strip($str);
    #info: strips off beginning and endings returns, newlines, tabs, a
+nd spaces
    my $str=shift;
    if(length($str)==0){return;}
    $str=~s/^[\r\n\s\t]+//s;
    $str=~s/[\r\n\s\t]+$//s;
    return $str;
    }
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