Modeling and simulating physical systems have given a lot of conveniences for researchers. The purpose of this work is to introduce a new physical modeling tool in Mat-lab/Simulink R2012b: 2nd Generation of SimMechanics in Simscape tool, and apply to build as well as to control a Biomechanical system: a powered gait training system designed for hemiplegic patients. Firstly, a brief introduction about Simscape and 2nd Generation in SimMechanics was shown. After that, in order to show a practical application of this tool, the process of building and converting the model of the powered gait system for hemiplegia patients from 3D software Inventor model to SimMechanics 2nd Generation was described. In addition, the modeled system is also controlled and made comparison the received results between using classical PID control and artificial intelligence Fuzzy Logic Control (FLC) method. The results showed that we could build a good physical model by using this new tool. Besides, the simulated results also characterized that FLC controller has the better performance compared to PID control method in term of response, disturbance rejection.