In first stage nonlinear regression parameter estimate and in second stage autocorrelation structure estimate and finally the generalized least square estimates the function model parameters.
References
Riazoshams, H., Midi, H., Sharipov, O. S.H, (2010). The Performance of Robust Two Stage Estimator in Nonlinear Regression with autocorrelated Error, Communications in Statistics - Simulation and Computation, 39: 1251-1268.