Quantum state preparation and especially quantum state reconstruction of mechanical oscillators is currently a significant challenge. Here we propose a scheme that employs short optical pulses to realize quantum state tomography, squeezing and state purification of a mechanical resonator. The scheme presented also allows observation of mechanical quantum noise despite preparation from a thermal state and is shown to be experimentally feasible. The proposal thus provides a promising means to explore the quantum nature of massive oscillators and can be used in other systems such as trapped ions.