In this paper, we aim to achieve two specific objectives. The first one is to examine the applicability of the Artificial Neural Networks (ANNs) technique in ore grade estimation. Different training algorithms and numbers of hidden neurons are applied to estimate Cu grade of borehole data in the hypogene zone of porphyry copper-gold deposit, Masjed-Daghi, East Azerbaijan Province (Iran). The efficacy of ANNs in function-learning and estimation is compared with ordinary kriging (OK). As the kriging algorithms smooth the data, their applicability in the pre-processing of data for fractal analysis is not conducive. ANNs can be introduced as an alternative for this kind of problem. Secondly, we aim to delineate the potassic and phyllic alteration regions in the hypogene zone of Cu-Au porphyry deposit based on the estimation obtained by the ANNs and OK methods, and utilize the Concentration-Volume (C-V) fractal model. In this regard, at first, C-V log-log is generated based on the ANN results. The plots are then used to determine the Cu threshold values for the alteration zones. To investigate the correlation between the geological model and C-V fractal results, the log ratio matrix is applied. The results obtained show that Cu values less than 0.38% from ANNs have more overlapped voxels with phyllic alteration zone by an overall accuracy of 0.72. Spatial correlation between the potassic alteration zones resulting from 3D geological modeling and high concentration zones in C-V fractal model show that Cu values greater than 0.38% have more voxels overlapped with the potassic alteration zone by an overall accuracy of 0.76. Generally, the results obtained show that a combination of the ANNs and C-V fractal methods can be a suitable and robust tool for quantitative modeling of alteration zones instead of the qualitative methods.