Charging effects in an AlxGa1-xN/GaN heterostructure field-effect transistor epitaxial layer structure have been studied using scanning capacitance microscopy. Voltages of less than or equal to 6 V applied between an AlxGa1-xN/GaN sample structure and a conducting proximal probe tip are found to create trapped charge in both doped and undoped heterostructures. Scanning capacitance measurements obtained over a wide range of bias voltages allow the charge distribution to be mapped both laterally and in depth with submicron to nanometer scale spatial resolution. Scanning capacitance imaging as a function of bias voltage performed in conjunction with numerical capacitance-voltage simulations suggests that positive charge can be trapped at the AlxGa1-xN surface and within the GaN layer and negative charge can be trapped at or near the AlxGa1-xN/GaN interface.