Virtual reality (VR) presents objects or simulated scenes to reproduce situations in a way that is very similar to the real thing. In medicine, processing and 3D reconstruction of medical images is an important step in VR that has had significant breakthroughs. We propose a methodology for processing medical images (DICOM), 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 DICOM image processing method based on area differentiation and 3D reconstruction by the `isodurface' and `alpha-shape' methods for the creation of a virtual environment in Blender. Different studies shows the benefits of VR applied to clinical practice, adding the uses they have as educational tool. Improved 3D segmentation and reconstruction methods are needed to obtain more detailed structures and better definition to be used in routine procedures.