In order to build an array of arrays you will need to use references.

my @masterarray = ( \@array1, \@array2, \@array3 );
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To cycle through them you can use some nested loops:

my $c = 0;
for my $a(@masterarray) { 
  print "Array: ", ++$c, "\n"; 
  print "  $_\n" for @$a;
}
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You may also want to investigate Data::Dumper. For more, see perldsc.