If you can hold everything in memory, this should come close to doing what you want. It has the following assumptions/behviors:

• Each row has the same number of whitespace delimited fields (columns).
• Zeroes starting a column or ending a column are meant to be zeroes after patching.

#!/usr/bin/env perl

use Modern::Perl;
use Data::Dump qw(pp);

my %cols;
my @patch_cols = qw(2 3);

while (<DATA>) {
    my @row = split;
    push @{$cols{$_}}, $row[$_] for (0..$#row);
}

for my $col (@patch_cols) {
    my @fwd = @{$cols{$col}};
    my @bwd = reverse @fwd;
    for my $i (1..$#fwd) {
        $fwd[$i] = $fwd[$i-1] if $fwd[$i] == 0;
        $bwd[$i] = $bwd[$i-1] if $bwd[$i] == 0;
    }
    @bwd = reverse @bwd;
    $fwd[$_] == $bwd[$_] and $cols{$col}->[$_] = $fwd[$_] for (0..$#fw
+d);
}

say pp(\%cols);
say pp(\@patch_cols);

__DATA__
1    100    1    2
101    200    1    2
201    300    1    0
301    400    1    0
401    500    0    2
501    600    0    2
601    700    0    0
701    800    1    1
801    900    1    2
[download]

Produces:

{
  "0" => [1, 101, 201, 301, 401, 501, 601, 701, 801],
  "1" => [100, 200, 300, 400, 500, 600, 700, 800, 900],
  "2" => [1, 1, 1, 1, 1, 1, 1, 1, 1],
  "3" => [2, 2, 2, 2, 2, 2, 0, 1, 2],
}
[2, 3]
[download]