open FILE1, 'file1' or die $!;
my @keys = <FILE1>;
chomp @keys;
my %keys = map { $_ => 1 } @keys;
close FILE1;

open FILE2, 'file2' or die $!;
open FILE3, '>file3' or die $!; # output file

print FILE3 grep { exists $keys{(split)[1]} } <FILE2>;

close FILE2;
close FILE3;