As you know, with a central air conditioning system, your air conditioner and furnace share the same ductwork and airflow route.
It is important to maintain the air quality. Filters are designed with more allergy-friendly features and the variety to choose from is good.
You may, however, consider upgrading to a high efficient filtration system. There are a few options which you could explore at http://www.weinstall.ca/air_quality.htm
Replacement filters are available at Filters Canada