Before factories release the waste gases into the air, filters are used to "deal with"/"process" emissions.
Even if they don't use filters, they do something to reduce the emissions or make the emissions less harmful. What are the verbs?
One quite sophisticated/advanced verb that you could use would be "to mitigate."
"Factories apply filters to mitigate the effects of the smoke that they emit."
to mitigate = to reduce the damaging effects of something.