We present a robust method to characterize the gravitational wave emission from the remnant of a neutron star coalescence. Our approach makes only minimal assumptions about the morphology of the signal and provides a full posterior probability distribution of the underlying waveform. We apply our method on simulated data from a network of advanced ground-based detectors and demonstrate the gravitational wave signal reconstruction. We study the reconstruction quality for different binary configurations and equations of state for the colliding neutron stars. We show how our method can be used to constrain the yet-uncertain equation of state of neutron star matter. The constraints on the equation of state we derive are complimentary to measurements of the tidal deformation of the colliding neutron stars during the late inspiral phase. In the case of a non-detection of a post-merger signal following a binary neutron star inspiral we show that we can place upper limits on the energy emitted.