Little shorter version (sorry, couldn't resist my perlgolfer soul...) - maybe you will find it useful.

#!perl -l

use strict;
use warnings;

use Data::Dumper;

my @data = <DATA>;
my $string = join" ", @data;

for(@data)
{
    my @array = split;
    print Dumper(@array);
}


__DATA__
Port         Alias            Oper     Admin   Speed  Duplex  Type
             (truncated)      Status   Status  (bps)
------------ ---------------- -------- ------- ------ ------- --------
+----------
vlan.0.4094                   up       up                     other
host.0.1                      up       up       10.0M         other
ge.1.1                        down     up       10.0M half    10-t    
+     rj45
ge.1.2                        down     up       10.0M half    10-t    
+     rj45
ge.1.3                        down     up       10.0M half    10-t    
+     rj45
ge.1.4                        down     up       10.0M half    10-t    
+     rj45
ge.1.5                        down     up       10.0M half    10-t    
+     rj45
[download]

But I do not know where you get empty column. I have run it, but I don't see any empty variables...