Removing sequences or OTUs from SELECTED groups only?

How can I delete sequences or OTUs from some of the sample groups only (not all of them)? Let’s say my data includes very different types of samples, and I want to remove potential contaminants only from low-biomass ones, but not from high-biomass ones.

I doubt there’s a function to do this in mothur because it’s fairly difficult to justify treating data differently for different samples. You could do it in R with some logic based filtering