Hello Hui,
Welcome to the forums! :qiime2:
There is a way to filter multiple taxa at the same time, however I think there's a better way to think about taxa that appear in your negative control.
ah... that might cause other problems. 
The Illumina platform suffers from index-hopping between samples, and the most abundant amplicons are the most likely to 'hop' into other samples because of a mismatched barcode. This means that a perfectly empty negative control would still get some reads assigned to it by the Illumina sequencer, and essentially be a tiny subset of all real amplicons. Because this happens during sequencing, real amplicons may end up in empty negative controls.
That's a much better idea! We have discussed some methods like this, and I think that's the way to go.
It looks like FEAST it still tagged as a beta, but you could still try and get support from the developer! You could also check out q2-quality-control or decontam, which have similar goals.