Multiple Sclerosis (MS) is a chronic autoimmune disease that affects the central nervous system. Nerves are covered by a layer called myelin, which is responsible for protecting and maintaining their functionality. In the case of MS, the myelin becomes damaged, resulting in the nerves functioning unpredictably. MS is a disease characterized by relapses, which can cause permanent and irreversible damage to the patient's mobility, vision, and sensations, unless appropriate medical treatment is administered in time. This highlights the importance of the early detection of the presence or differentiation of MS using computer assisted diagnosis (CAD) systems. This study proposes an automatic segmentation approach of MS damaged regions using deep neural networks that can be integrated with any 3rd party CAD system. The data utilized comprised of a total of 1838 T2-type Magnetic Resonance Imaging (MRI) images collected from a cohort of 38 patients who underwent imaging at two distinct time points. Each MRI image was accompanied by meta-data, detailing the specific locations of the observed damage attributed to MS. The experimental setup investigated and optimized a comprehensive combination of different data preprocessing and augmentation steps, using several variations of the U-Net convolutional neural network (CNN), like U-Net++, Attention U-Net, ResUNet-a and TransUNet. The proposed methods achieved a segmentation accuracy of 0.70 based on the Dice Similarity Coefficient (DSC), a performance comparable to 2D and 3D state-of-the-art approaches in literature. A software framework encapsulating the automated model was also developed to facilitate the clinical practice workflow and underpin adoption by medical practitioners.