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Due to the computational cost of calculating a great number of variations of the parameters, detailed radiative models of pulsar wind nebulae (PWNe) do not usually contain fitting algorithms. As a consequence, most of the models in the literature are, in fact, qualitative fits based on visual inspection. This is particularly true when complex, time-dependent models are considered. Motivated by improvements in the computational efficiency of the current PWN models that were obtained in the last years, we here explore the inclusion of automatic fitting algorithms into a fully time-dependent model. Incorporating an efficient fitting tool based on the Nelder-Mead algorithm, we blindly find fitting solutions for the Crab nebula and 3C 58 with a time-dependent radiation model to compute the spectral and dynamical evolution of young and middle-aged PWNe. This inclusion allows us, in addition of more faithfully determining the quality of the fit, to tackle whether there exist degeneracy in the selected PWNe models. We find both for Crab and 3C58, that the fits are well determined, and that no other significantly different set of model parameters is able to cope with experimental data equally well. The code is also able to consider the system's age as a free parameter, recursively determining all other needed magnitudes depending on age accordingly. We use this feature to consider whether a detailed multi-frequency spectra can constrain the nebula age, finding that in fact this is the case for the two PWNe studied.