my %hash;
open my $IN2, "<", $file2 or die "could not open $file2 $!";
while (my $line = <$IN2>) {
    chomp $line;
    next if $line =~ /^\s*$/; # skip empty line
    $hash{$line} = 1;
}
close $IN2;
open my $IN1, "<", $file1 or die "could not open $file1 $!";
open my $OUT, ">", $file3 or die "could not open $file3 $!";
while (my $line = <IN1>) {
    chomp $line;
    next if $line =~ /^\s*$/;
    print $OUT "$line\n" if exists $hash{$line};
}
close $IN1;
close $OUT;