Reading between the lines, I think he meant

($AoA) = @_;
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but meant to call the function using a reference

&PrintArray2(\@FruitArray);
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Once more I point out that using use strict and -w would have caught this error.

Update: tye's fixes do, of course, work. But I think that the intention was that the second example would involve passing the array to the sub as reference. In that case, the second sub is very broken. Here's a fixed version (which also passes -w and use strict).

#!/usr/local/bin/perl -w

use strict;

#Load Array
my @FruitAoA = ([qw/Fruit Apple Red/],
                [qw/Fruit Bananna Yellow/],
                [qw/Fruit Orange Orange/],
                [qw/Fruit Kiwi Green/]);

&PrintArray;
&PrintArray2(\@FruitAoA);

#Print Array with Array Name Hardcoded
sub PrintArray {
  for my $i ( 0 .. $#FruitAoA ) {
    for my $j ( 0 .. $#{ $FruitAoA[$i] } ) {
      print "$FruitAoA[$i][$j]\n";
    }
  }
}

#Trying to Print Array by Reference
sub PrintArray2 {
  my ($AoA) = @_;
  for my $i ( 0 .. $#{$AoA} ) {
    for my $j ( 0 .. $#{ $AoA->[$i] } ) {
      print "$AoA->[$i][$j]\n";
    }
  }
}
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"Perl makes the fun jobs fun
and the boring jobs bearable" - me