While modeling nonlinear systems by combining a linear model with a nonlinear compensation term, namely, virtual unmodeled dynamics (VUD), the parameter estimation of the linear model and the learning-based VUD estimate influences and interacts with each other simultaneously. This paper aims to develop an alternating identification scheme for resolving such a challenging problem, where a projection algorithm is employed to identify the linear model and a feedforward neural network is used to model the VUD of a class of nonlinear dynamical systems. An open-loop estimation algorithm on the VUD is first presented under the known linear model, followed by an alternating identification algorithm for completely unknown nonlinear systems. Algorithm description is given and some simulation studies on multiple input and multiple output nonlinear systems are carried out to illustrate the effectiveness of our proposed modeling techniques.