Can you use an air cleaner/purifier while also using aromatherapy?

I love using aromatherapy (but very new to it) and currently I am using a small gl dish with a tea-light to heat the oils. Now I want to get an air filter/purifier to clean the air in my home office (where I also use the aromatherapy oils). When I use the air cleaner/purifier, will it "clean" the scent of my aromatherapy, basically making it useless and a waste to heat the oils?