Medical images have noise, such as salt and pepper, speckle, and gaussian noise. So, getting the accuracy of magnetic resonance images is challenging always. The accuracy of brain images is essential for the clinical diagnosis process. The nonlinear method of median and morphological filters is used for enhancement, contrast adjustment, and histogram equalization for medical images and speech processing, to preserve them from noise and edge features. Because of its edge-preserving properties, this median spatial filter window is critically important and better for removing impulsive noise and speckle noise. Nine different shapes of windows and five different sizes of windows and five noise density injections are used for evaluating the performance of the median filter. The first person J.W.Tukey, did the smoothing process by median rank selection filter. The denoising using morphological process is also considered for analysis. These two nonlinear methods like median filtering and morphological methods are used for the restoration of noise from the original image. These two methods are applied in normal and seizure-affected images to calculate quality assessment metrics and also the performance evaluation metrics from magnetic resonance images. Any image needs to be denoised to get the accuracy, precision, and F-measure kind of common feature evaluation metrics. This paper evaluates two nonlinear filtering methods and their performance evaluated based on shapes and size of windows and for suppressing or de-noising to produce original noise-free images to assist clinically.