It's not very clear exactly what your program needs to do, but I think you want something a bit like this.

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;
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