Hi @laoshiren,
Gotcha! Sorry I must have not read your original question carefully.
The short answer is no, there is currently no way of filtering the FeatureData[Taxonomy], though it is an issue raised for future implementation. I’m guessing it is not a matter of priority in development though because extra taxa in those artifacts don’t affect downstream use. For example, if you are assigning taxonomy to your feature table the extra taxa would just not be used, no error will be raised.
May I ask why you need those filtered from your taxonomy artifact? You can always filter these outside of qiime2 if you really need them, the post here has some suggestions as far as doing this.