Software estimation involves meeting a huge number of different requirements, such as resource allocation, cost estimation, effort estimation, time estimation, and the changing demands of software product customers. Numerous estimation models try to solve these problems. In our experiment, a clustering method of input values to mitigate the heterogeneous nature of selected projects was used. Additionally, homogeneity of the data was achieved with the fuzzification method, and we proposed two different activation functions inside a hidden layer, during the construction of artificial neural networks (ANNs). In this research, we present an experiment that uses two different architectures of ANNs, based on Taguchi’s orthogonal vector plans, to satisfy the set conditions, with additional methods and criteria for validation of the proposed model, in this approach. The aim of this paper is the comparative analysis of the obtained results of mean magnitude relative error (MMRE) values. At the same time, our goal is also to find a relatively simple architecture that minimizes the error value while covering a wide range of different software projects. For this purpose, six different datasets are divided into four chosen clusters. The obtained results show that the estimation of diverse projects by dividing them into clusters can contribute to an efficient, reliable, and accurate software product assessment. The contribution of this paper is in the discovered solution that enables the execution of a small number of iterations, which reduces the execution time and achieves the minimum error.