I think you've got it pretty much covered Chady and Caron.

The lines are a section of hex from a Windows registry file & the 39's are the first four digits of a user's access code to use a specific color laser printer. I'm reading a code in based on username and trying to replace the four 9's with each user's specific code.

The fact that it's on multiple lines is definately part of my problem. I also was trying to escape my \n characters as well. I didn't realize I could each value without specifying the whole line. Here is my finished output:

#!/usr/bin/perl
open (USERS, "user.txt") or die "Cannot open file user.txt: $!\n";
@users = (<USERS>);
close USERS;

foreach (@users){
    chomp;
    ($userid,$acode) = split/\|/;
    if ($userid eq $ENV{"USERNAME"}) {
        @fields = split //, $acode;

        open(REG, "template.reg") or die "Cannot open file template.re
+g: $!\n";
        @hex =(<REG>);;
        close(REG);

        open(NEWREG, "> import.reg") or die "Cannot open file import.r
+eg: $!\n";
        foreach $line (@hex){
            my $i = 0;
            $line =~ s/,39,/,3$fields[$i++],/g;
            print NEWREG "$line";

        }
        close(NEWREG);
    }
}
[download]

Thanks for the assistance!