my $analysis_file = shift;

open INFILE_1, '<', $analysis_file
    or die "Can't open '$analysis_file': $!\n";

while(<INFILE_1>) {
    my $ALL_FT_FILE = $_; # or some part of $_ after munging

    open INFILE_2, '<', $ALL_FT_FILE
        or die "Can't open '$ALL_FT_FILE': $!\n";

    while(<INFILE_2>) {
        ...  # is the outer $_ clobbered here?
    }
}

##</code><code>##

open O, '>', 'foo';
print O "bar\n";
close O;
open O, '>', 'bar';
print O "$_\n" for qw(foo quux wrdlbrmfd);
close O;

open I, '<', 'foo';
while (<I>) {
    chop;
    open II, '<', $_ if -f $_;
    while (<II>) {
        print;
    }
    print "\$_ = '$_'\n";
}
__END__
foo
quux
wrdlbrmfd
$_ = ''