Model-based System Engineering (MBSE) is proved an effective way to develop complex systems, and lots of MBSE methods/tools have been developed in recent years. Lack of deep analysis of mainstream MBSE methods/tools and guidance in performing MBSE under the general SE process leads to a rough patch for design staff to transform from document-based system engineering to model-based system engineering. In this paper, step-by-step modelling practice following the official tutorials is performed to analyze MagicGrid (MagicDraw), ARCADIA (Capella), and HarmonySE (Rhapsody). This is the first time to analyse the mainstream MBSE methodolgies from the uniform INCOSE SE practice view and compare the method and modeling tool differences. These will provide a detailed guide for the engineers to transform from document-based system engineering to model-based system engineering.