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.

In reply to Re: arrays of arrays by toolic
in thread arrays of arrays by monkantar

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.