A system and method of performing a high speed filtering of data by using a GPU is disclosed. According to embodiments of the present invention, the system and method of processing data by using a graphic processing unit (GPU) including a video memory comprising multiple blocks, comprises: acquiring an image frame including a plurality of pixels representative of a target object; receiving a user input for processing the image frame; grouping each predetermined number of the pixels of the image frame into a group; uploading each of the groups to a respective block of the video memory; and performing operations on the groups uploaded to the video memory based on the user input.