We investigated student difficulties in learning quantum mechanics in an upper division quantum course at the University of Maryland. A set of exam questions and interviews has been developed to probe student understandings of the quantum wavefunction. We find that many students are confused about the relation between the wavefunction and the kinetic energy and often appear to interpret the wave function as an energy. They often display a strong "friction-like" model in which the wave function "loses energy" in tunneling through a barrier. We will report our findings in detail and discuss the student performance under modified instruction.