Medical images of a brain, acquired with computer tomography (CT) and magnetic resonance (MR) are widely used in medicine for patient diagnosis. To diagnose the patient it is relevant to analyze the pathology zones of the medical image and estimate their volume. The standard software for processing MR and CT images in many cases does not meet the requirements of physicians (problems with pathology zone extraction and volume estimation). Therefore, a task of medical image pathology zone volume estimation develops in medical image analysis. To solve this task, an efficient volume estimation method for evaluating volume of the pathology zones is proposed in this work. The proposed approach uses the data of 3D brain model, which is rebuilt from 2D medical images. The developed method can be used to obtain volume of the pathology zone with high precision and provide practical improvements to the reliability of medical diagnostics.