A major pharmaceutical intervention for management of many infectious diseases is the use of antiviral drugs. However, the rise of drug resistance poses significant threats to the effectiveness of drugs. This research proposes to determine optimal treatment strategies, through the development of population dynamical models for disease transmission and control, which can minimize the effect of resistance emergence in the population. This work will primarily focus on influenza infection, which still inflicts substantial morbidity, mortality, and socioeconomic costs worldwide.