for (@MainArray) {
    @$_ = grep { ! /[a-z]/ } @$_;
}

##</code><code>##

#!/usr/bin/env perl

use strict;
use warnings;

use Data::Dumper;

my @MainArray;

# Original array populating code
while (<DATA>) {
    chomp;
    push @MainArray, [ split // ];
}

# New alternative to 'splice' code
for (@MainArray) {
    @$_ = grep { ! /[a-z]/ } @$_;
}

print Dumper \@MainArray;

__DATA__
Hello
my
name
is
Jack

##</code><code>##

$ pm_file_chars_to_AoA_2.pl
$VAR1 = [
          [
            'H'
          ],
          [],
          [],
          [],
          [
            'J'
          ]
        ];