sub grep2d {
  my($ar, $el) = @_;
  grep { grep $el == $_, @$_ } @$ar;
}

use Data::Dumper;
my $array = [ [ 1 .. 3 ], [ 4 .. 5 ], [ 3 .. 5 ] ];
print Dumper( grep2d($array, 3) );

__output__

$VAR1 = [
          1,
          2,
          3
        ];
$VAR2 = [
          3,
          4,
          5
        ];