Virtual reality (VR) presents objects or simulated scenes to reproduce situations in a way similar to the real thing. In medicine, processing and 3D reconstruction of medical images is an important step in VR. We propose a methodology for processing medical images, to segment organs, reconstruct structures in 3D and represent structures in a VR environment, in order to provide the specialist with an alternative tool for the analysis of medical images. We present a method of image segmentation based on area differentiation and other image processing techniques; the 3D reconstruction was by the 'isosurface' method. Different studies show the benefits of VR applied to clinical practice, adding its uses as an educational tool. A VR environment was created to be visualized with glasses for this purpose, this can be an alternative tool in the identification and visualization of COVID-19 affected lungs through medical image processing and subsequent 3D reconstruction.