I see hdb has shown the syntax you requested. Be aware that splice can be slow and there are often better alternatives. For instance, if you had intended to use splice to remove lowercase characters, you could have rewritten that entire block of code above as:

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

Here's my test:

#!/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
[download]

Output:

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