Here's a splitting and unpacking option for your data set that puts the desired elements into an array:

use Modern::Perl;

for ( grep /\S/, <DATA> ) {
    my @data = ( split /\./ )[ 0 .. 3 ];
    splice @data, 1, 1, unpack '(a4)(a2)*', $data[1];
    say "@data";
}

__DATA__
3B40RT.2000033121.7.bin.gz
3B40RT.2000033121.7R.bin.gz
3B40RT.2000033121.7RWER.bin.gz
[download]

Output:

3B40RT 2000 03 31 21 7 bin
3B40RT 2000 03 31 21 7R bin
3B40RT 2000 03 31 21 7RWER bin
[download]