I believe you could easily use grep in your subroutine, as in:

sub remove_poly
{
    my ($array,$lim) = @_;

    my $len = length $array->[0];
    my @sel_array = grep {
       my $a_count = $_ =~ tr/A//;
       my $t_count = $_ =~ tr/T//;
       my $c_count = $_ =~ tr/C//;
       my $g_count = $_ =~ tr/G//;

       my $a_portion = $a_count/$len;
       my $t_portion = $t_count/$len;
       my $c_portion = $c_count/$len;
       my $g_portion = $g_count/$len;

       $_ if ( $a_portion < $lim && $t_portion < $lim && $c_portion < 
+$lim && $g_portion < $lim )
    } @$array;
    return @sel_array;
}
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The initial array being big, you could also return a reference to the resulting set, instead of the whole array.