It is well known that learners using intelligent learning environments make different use of the feedback provided by the intelligent learning environment and exhibit different patterns of behaviour. Traditional approaches to measuring such behaviour have focused on observational methods, think-aloud protocols, ratings and log data. More recently, the field of educational neuroscience has placed greater emphasis on real-time measures using eye tracking, electroencephalogram and functional magnetic resonance imaging. Our work fits into the latter vein. Drawing on a literature review from cognitive psychology, neuroscience and education, we describe our Learner Processing of Feedback in Intelligent Learning Environments model of how learners process feedback. We also present findings from a pilot study as a preliminary test of the model. Seventeen learners participated in an experiment using the intelligent learning environment known as Crystal Island. A range of data was collected, including a pre-test measuring prior knowledge, think-alouds, log data, video recordings, biometrics and post-task questionnaires. We discuss these findings and steps forward to further validate the model using physiological measures.