Abstract: A control system and method utilize an intake manifold absolute pressure (MAP) and an engine speed (RPM) sensor and a controller configured to obtain a model surface relating various measurements of the RPM sensor and valve overlap durations to modeled scavenging ratios of an engine, obtain a calibrated multiplier surface relating various measurements of the MAP and RPM sensors to measured scavenging ratios of the engine, determine a modeled scavenging ratio of the engine based on the measured engine speed and a known overlap duration using the model surface, determine a scavenging ratio multiplier based on the measured MAP and measured engine speed using the calibrated multiplier surface, determine the scavenging ratio of the engine by multiplying the modeled scavenging ratio by the scavenging ratio multiplier, and control the engine based on the scavenging ratio.