Stabilizing the complexity of Feedforward Neural Networks (FNNs) for the given approximation task can be managed by defining an appropriate model magnitude which is also greatly correlated with the generalization quality and computational efficiency. However, deciding on the right level of model complexity can be highly challenging in FNN applications. In this paper, a new Model Selection algorithm using Binary Ant Colony Optimization (MS-BACO) is proposed in order to achieve the optimal FNN model in terms of neural complexity and cross-entropy error. MS-BACO is a meta-heuristic algorithm that treats the problem as a combinatorial optimization problem. By quantifying both the amount of correlation exists among hidden neurons and the sensitivity of the FNN output to the hidden neurons using a sample-based sensitivity analysis method called, extended Fourier amplitude sensitivity test, the algorithm mostly tends to select the FNN model containing hidden neurons with most distinct hyperplanes and high contribution percentage. Performance of the proposed algorithm with three different designs of heuristic information is investigated. Comparison of the findings verifies that the newly introduced algorithm is able to provide more compact and accurate FNN model.