Interesting ... if I'm reading the OP correctly, you want to create a looping structure that is influenced in two ways by a command line argument: first, the number of loops is controlled by the length of the command line argument; and two, what you're looping is controlled by the command line argument.

So if the command line argument is CV, you loop as such:

  foreach my $con ( @consonants ) {
     foreach my $vow ( @vowels ) {
        ..
     }
  }
[download]

and if the command line argument is CVCCVC, you loop as such:

    foreach my $con_1 ( @consonants ) {
      foreach my $vow_1 ( @vowels ) {
        foreach my $con_2 ( @consonants ) { 
          foreach my $con_3 ( @consonants ) {
            foreach my $vow_2 ( @vowels ) {
              foreach my $con_4 ( @consonants ) {
                ...
              }  
            } 
          } 
        } 
      }
    }
[download]

is that correct?

My first reaction is find another way. But if you wish to persist, I think recursion is your frenemy here:

#!/usr/bin/perl

my $template   = shift || die "usage: $0 <template>\n";
my @pattern    = split( //, $template );
my $levels     = scalar( @pattern );

my $vowels     = [ qw( a e i o u y ) ];
my $consonants = [ qw( b c d f g h j k l m n p q r s t v w x z ) ];

output_cv( 0, \@pattern, $consonants, $vowels, "" );

sub output_cv {
  my( $level, $pattern, $consonants, $vowels, $string ) = @_;

  # if we have no more levels in the pattern, output the buffered stri
+ng
  if( $level == scalar( @$pattern ) ) {
    print "$string\n";
  } else {
    # figure out which array at this pattern level
    my $array = $pattern->[$level] eq 'C' ? $consonants : $vowels; 

    foreach my $ele ( @$array ) {
      # start new buffer string
      my $new_string = $string . $ele;
      # recurse to next level
      my $new_level = $level + 1;
      output_cv( $new_level, $pattern, $consonants, $vowels, $new_stri
+ng );
    }
  }
}
[download]

I say frenemy because the above is a fairly naive implementation and eventually some combination of template size and/or arrays is going to blow the stack.

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