#! perl -slw
use strict;
use List::Util qw[ max ];
use Data::Dumper::SLC;

my @cmat = (
	[ qw[ A B C F G ] ],
	[ qw[ u b  ] ],
	[ qw[ 1 T A R S 2 P] ],
);

my @trans = map {
	my $index = $_;
	[ map{ $_->[ $index ] } @cmat ];
} 0 .. max map{ $#$_ } @cmat;

Dump \@trans;
__END__
P:\test>junk
[
    [ 'A', 'u', '1',  ],
    [ 'B', 'b', 'T',  ],
    [ 'C', undef, 'A',  ],
    [ 'F', undef, 'R',  ],
    [ 'G', undef, 'S',  ],
    [ undef, undef, '2',  ],
    [ undef, undef, 'P',  ],
]