Presumably, you wanted to operate on the locations which contained "0" values.

Here is code that shows how to do so:

#!/usr/bin/perl -w
use strict;

my (@one,@two,@three,@four);

for (\@one,\@two,\@three,\@four){
  # Populate them
  @$_ = map {int (rand() * 10)} 0..499;
}

my $zerocount = 0;
my $index = 0;
my $array = 0;

for (\@one,\@two,\@three,\@four){
  # Look for zero, and change it to 999.
    $index = -1;
    for (@$_){
       $index ++;
       next unless $_ == 0;
       print " Found a zero in array $array at $index.  inserting 999\
+n";
       $_ = 999; # Changes the value!!!!
    }
    $array ++; 
}
[download]