In this work we investigate a generic method able to extract information on molecular organization in biological samples from polarized second harmonic generation (SHG) microscopy, without the need to infer an a priori model for the molecular orientational distribution. The mean orientation of this distribution, as well as its first and third orders of symmetry, are estimated by monitoring SHG intensity signals under a varying incident polarization. We introduce, in particular, a reduction of the problem to a two-dimensional approach appropriate to the microscopy geometry. This method allows us to retrieve determining information which is not available in the traditional model-oriented methods, as illustrated in molecular-order imaging in collagen fibrils. The precision of the parameters estimation is evaluated by a Monte Carlo analysis, based on the Poisson noise statistics of the measured signal.