I might use the Text::CSV module to parse and compose CSV, perhapse something like the following:

use strict;
use warnings;
use Data::Dumper;
use IO::String;
use Text::CSV;

my $file1 = IO::String->new(<<EOF) or die "$!";
username, date_modified
2010-nhw-es-ea-285, 2012-10-10
aab.external.audit.-.bvr.verif.externes, 2012-02-22
aashee.aziz, 2012-01-27
abbas.rangwala, 2012-01-27
abbie.gardner, 2012-09-10
ab.border-frontiere, 2012-08-11
abdool.yasseen, 2012-01-31
abdullah.aboukarr, 2012-08-10
abdullahi.sheikh, 2012-02-28 
EOF

my $file2 = IO::String->new(<<EOF) or die "$!";
fullname, branch
aaron.northway, CHIEF FINANCIAL OFFICER BRANCH
aashee.aziz, HEALTH PRODUCTS AND FOOD BRANCH
abbey.klugerman, HEALTHY ENVIRONMENTS AND CONSUMER SAFETY BRANCH
abby.hoffman, STRATEGIC POLICY BRANCH
abderrahim.boussanni, CHIEF FINANCIAL OFFICER BRANCH
abdiaziz.nur, HEALTHY ENVIRONMENTS AND CONSUMER SAFETY BRANCH
abdool.yassin, HEALTH PRODUCTS AND FOOD BRANCH
abdoulie.manjang, N/A
abdullah.hassen, HEALTH PRODUCTS AND FOOD BRANCH
abdullah.patel, REGIONS AND PROGRAMS BRANCH
asdf "asdf" asdf,,
EOF


my $csv1 = Text::CSV->new({
    binary  => 1,
    allow_whitespace    => 1,
    sep_char    => ',',
});

my %date_modified_by_username;
$csv1->column_names( $csv1->getline($file1) );   # get header line
while(my $href = $csv1->getline_hr($file1)) {
    $date_modified_by_username{$href->{username}} = $href->{date_modif
+ied};
}


my $csv2 = Text::CSV->new({
    binary  => 1,
    allow_whitespace    => 1,
    sep_char    => ',',
    eol => "\n",
});

$csv2->print(\*STDOUT, [ qw{username branch date_modified} ]);

$csv2->column_names( $csv2->getline($file2) ); # get header line
while(my $href = $csv2->getline_hr($file2)) {
    my $date_modified = $date_modified_by_username{$href->{fullname}}
        || 'unknown';
    
    $csv2->print(\*STDOUT, [
        $href->{fullname}, $href->{branch}, $date_modified
    ]);
}
[download]

With your sample data this produces:

username,branch,date_modified
aaron.northway,"CHIEF FINANCIAL OFFICER BRANCH",unknown
aashee.aziz,"HEALTH PRODUCTS AND FOOD BRANCH",2012-01-27
abbey.klugerman,"HEALTHY ENVIRONMENTS AND CONSUMER SAFETY BRANCH",unkn
+own
abby.hoffman,"STRATEGIC POLICY BRANCH",unknown
abderrahim.boussanni,"CHIEF FINANCIAL OFFICER BRANCH",unknown
abdiaziz.nur,"HEALTHY ENVIRONMENTS AND CONSUMER SAFETY BRANCH",unknown
abdool.yassin,"HEALTH PRODUCTS AND FOOD BRANCH",unknown
abdoulie.manjang,N/A,unknown
abdullah.hassen,"HEALTH PRODUCTS AND FOOD BRANCH",unknown
abdullah.patel,"REGIONS AND PROGRAMS BRANCH",unknown
[download]