Hi @Nisha,
Would you mind posting your solution, so that others on the forum can benefit?
There are a variety of ways to do this as outlined in the filtering documentation , specifically about filtering sequences.
For example if you wanted to remove plastid sequences you could do:
qiime taxa filter-table \
--i-table ./table.qza \
--i-taxonomy ./taxonomy.qza \
--p-mode 'contains' \
--p-include 'p__' \
--p-exclude 'p__;,Eukaryota,Chloroplast,Mitochondria,Unassigned,Unclassified' \
--o-filtered-table ./table-no-ecmu.qza
More details can be found here, and here.
If you want to check for and remove chimeras from your data you can use vsearch. Check out this chimera removal tutorial. In case you are performing OTU clustering, etc... you can look through the clustering sequences tutorial too.
-Cheers!