grep is one way:

use warnings;
use strict;
use Data::Dumper;

my @positions = (
    [qw(1 A)],
    [qw(2 A)],
    [qw(3 G)],
    [qw(4 T)],
    [qw(5 C)],
);

@positions = grep { (@{ $_ })[1] !~ /^[GC]/ } @positions; 

print Dumper(\@positions);

__END__

$VAR1 = [
          [
            '1',
            'A'
          ],
          [
            '2',
            'A'
          ],
          [
            '4',
            'T'
          ]
        ];
[download]

See also:

• perldsc

UPDATE: Seeing aitap's solution reminds me of simpler syntax:

@positions = grep { $_->[1] !~ /^[GC]/ } @positions;
[download]