Your question is a little ambiguous regarding the exact format of your input file, and your desired output, but I refactored your code as shown below:

> cat input.txt
book 1 pencil 2 desk 3
foo 5 bar 6 baz 7
>
> cat 637646.pl
#!/usr/bin/env perl
 
use warnings;
use strict;
 
my (@n, @w);
 
open INFILE, '<', 'input.txt' or die "can not open file $!\n";
while (<INFILE>) {
    my (@numbers) = /(\d+)/g;
    my (@words)   = /([a-z]+)/g;
    push @n, @numbers;
    push @w, @words;
}
close INFILE;
 
open  MYFILE, '>', 'output.txt' or die "can not write to file $!\n";
print MYFILE "$_ " for @n;
print MYFILE "\n";
print MYFILE "$_ " for @w;
print MYFILE "\n";
close MYFILE;
 
>
> 637646.pl
>
> cat output.txt
1 2 3 5 6 7
book pencil desk foo bar baz
>
[download]

The input file has a couple of lines, each with a few word-number pairs. The output was formatted with all numbers on one line and all words on the next line.

The does not employ arrays of arrays because I do not think that is necessary. Hope this helps.