Nowadays distance measures techniques have been quickly developed and widely used to the real application. The main objective of this thesis is to make a brief introduction of different distance measures methods, especially spike-time distance and its application to point pattern prototypes and Multi-Dimensional Scaling (MDS) methods. Meantime, R programming packages for spike-time distance, prototype and Multi-Dimensional Scaling have also been introduced in order to make these methods more practical and convenient to the real world. And, their packages are used to a real dataset as an application.