1. Load the smaller (to-be-removed) list into a hash, having stripped any extraneous bits (eg. say $line =~ s[</+$][];) and having lc'd them.
2. Read the bigger file line by line; strip any extraneous bits & lc them; if email read exists in the toBeRemoved hash, don't print it; otherwise do.
3. Redirect the output to a temp file. Delete the original master file; rename the temp file to the master.

If I'm understanding your issue, you have two data sets. One contained in removelist.txt:

user1@example.com
user3@example.com
...
[download]

The other in masterlist.txt:

user1@example.com
user2@example.com
user3@example.com
USER1@EXAMPLE.COM<mailto:USER1@EXAMPLE.COM>
user4@example.com
user5@example.com
user5@example.com<mailto:user5@example.com>
...
[download]

You want items from the first set to be removed from the second. Excellent suggestions have been offered, and this is a "classic issue."

See if the following will work for your situation:

use Modern::Perl;
use File::Slurp qw/ read_file write_file /;

my $removeList = join '|',
    map { chomp; $_ } read_file 'removelist.txt';
    
write_file 'finallist.txt',
    grep !/$removeList/i, read_file 'masterlist.txt';
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With the above two data sets, here is the output to finallist.txt:

user2@example.com
user4@example.com
user5@example.com
user5@example.com<mailto:user5@example.com>
[download]

The script only does what you mentioned, viz., joins the removelist.txt items with the pipe character (alternation operator) for a !"or" regex of email addresses used by grep on the masterlist.txt lines.

Hope this helps!

To get a more efficient regular expression, use Regexp::Assemble to make your RE.

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

My blog: Imperial Deltronics

An excellent suggestion, CountZero...

What have you tried using Perl?
Really, there is no way, one can help except giving "assumed" examples, since no code, examples, likes or modified script was not given.
However, if this might help.
Get all the user from the masterlist.txt, then iterate through the removelist.txt, to remove from the masterlist hash, names contained in the removelist that matches. Then print out all the remaining users in the masterlist hash.

UPDATE:
Please, if I may illustrate the point above, using an example that could help.
Note:
This might not be the perfect example, but am sure it will give up a head up.
masterlist.txt

barak
osama
bush
jonathan
perl
python
java
c++
[download]

osama
jonathan
python
java
[download]

#!/usr/bin/perl
use warnings;
use strict;

my %new_list;

read_n_work_file( 'masterlist.txt', sub { undef $new_list{ $_[0] } } )
+;

read_n_work_file( 'removelist.txt',
    sub { delete $new_list{ $_[0] } if exists $new_list{ $_[0] } } );

print join "\n" => keys %new_list; # print to a new file

sub read_n_work_file {
    my ( $file, $workout ) = @_;

    open my $fh, '<', $file or die "can't open file:$!";
    while (<$fh>) {
        chomp;
        $workout->($_);
    }
}
[download]

bush
barak
perl
c++
[download]

Small suggestion/hint

perlmonks search, enter: "compare 2 files" and "compare two files"

Refer to the FAQ: perldoc -q "How do I compute the difference between two arrays?"

Thanks everyone for your assistance. There's certainly should be enough pointers for me to figure out this problem.