@Mikgar,
Sorry it looks like nobody ever answered your question — I think it came in during a busy travel period for the moderators so must have slipped past our radar.
If you want to isolate V3 regions prior to denoising, you can use qiime cutadapt trim-paired or trim-single with the --p-discard-untrimmed option... though that will only work if the primer is in the read.
If you want to isolate after denoising (or reads are not in the primer so you need to), you can use qiime quality-control exclude-seqs to align against sequences of interest (like V3 regions extracted from your reference database with qiime feature-classifier extract-reads)
You could also do this outside of QIIME 2 (e.g., before importing)... that would be the way to do it if (a) you want to separate before denoising/OTU clustering and (b) primers are not in the reads. VSEARCH is the tool I'd recommend for aligning fastq sequences against a reference database, and @Lauren's suggestion would work as well.
@Lauren thanks for responding, sharing a solution, and bringing this question back to our attention!