Multizone network airflow analysis is used to analyze stack and mechanical system effects on the distribution of three representative biological agents in a prototype 40 story building. This approach relies on mass balances to compute airflow and contaminant transfer between the building zones. The analysis considers stack effects caused by cold outdoor temperatures, unintended positive and negative pressurization of the floor on which the release of the agent occurs, and three levels of contaminant removal using a combination filter/UVGI system. The results show that vertical shafts, such as stairwells and elevator shafts provide significant routes for contaminant transfer between floors, even when these floors are served by different air handling systems. Because the air moving through these pathways does not pass through an air handling system, this type of transport is not as easily reduced by filtering. However, commercially available filters were able to reduce contaminant concentrations substantially in zones that receive contaminants primarily due to recirculation through the air handling system.