I'm not sure you really want to do what you think you are doing. Your code would be much cleaner, faster, and do what you mean if you kept it all in one script and used subs, like so:

use strict; use warnings;

my @array1 = ( 1 .. 3 );
my @array2 = ( 4 .. 6 );

print2arrs( \@array1, \@array2 );

sub print2arrs {
  my ( $ref1, $ref2 ) = @_;
  print @$ref1;
  print @$ref2;
}
[download]

And if you really do need to keep them in separate files, check out require or do to avoid using the system command and firing off an entirely new perl interpreter