I'm very a new comer to PHP and seeking to choose data from the MySQL area (inside a table). I made use of the next query.

$token = $wpdb->query("SELECT ami_st_token_aut 
                         FROM $wpdb->users 
                        WHERE ID = '".$current_user->ID."' ");

The worthiness within the ami_st_token_aut is really a large number however when i echo $token, it's echoing out $current_user->ID rather than the large token number. What is failing?

Two methods for doing the work.

If you are doing the work with WordPress, make use of the wpdb->prepare function:

$token = $wpdb->get_var(
  $wpdb->prepare(
    "SELECT ami_st_token_aut FROM $wpdb->users WHERE ID=%d", $current_user->ID
  )
);

If you are doing the work without Wordpress, make use of the mysql_real_escape_string function.

mysql_query(
  "SELECT ami_st_token_aut FROM tablename WHERE ID='" 
  . mysql_real_escape_string($ID) . "'"
);

See the Wordpress Codex.

The $wpdb->query function returns the amount of rows that matched up your query (should you perform a Choose, anyway).

$wpdb->get_var may be the function to make use of to obtain a single value in the database.

See this http://www.w3schools.com/php/php_mysql_select.asp about query execution