A system includes a residual per cylinder calculation module that calculates an amount of residual (i.e., trapped exhaust gas) within an engine cylinder. A temperature calculation module calculates a temperature within the engine cylinder based on the amount of residual. A first air per cylinder (APC) calculation module calculates total charge content within the engine cylinder based on the temperature and calculates a first amount of air trapped within the engine cylinder based on the total charge content and the amount of residual. A residual mass fraction (RMF) calculation module calculates an RMF of the exhaust gas based on the amount of trapped exhaust gas at EVC and the total charge content. A second APC calculation module determines a backflow of the charged content into the engine cylinder and calculates a second amount of air trapped within the engine cylinder based on the backflow and the first amount of air.