This textbook introduces the intellectual framework for modeling with Comsol Multiphysics, a package which has unique features in representing multiply linked domains with complex geometry, highly coupled and nonlinear equation systems, and arbitrarily complicated boundary, auxiliary, and initial conditions. But with this modeling power comes great opportunities and great perils. Progressively, in the first part of the book the novice modeler develops an understanding of how to build up complicated models piecemeal and test them modularly. The second part of the book introduces advanced analysis techniques. The final part of the book deals with case studies in a broad range of application areas including nonlinear pattern formation, thin film dynamics and heterogeneous catalysis, composite and effective media for heat, mass, conductivity, and dispersion, population balances, tomography, multiphase flow, electrokinetic, microfluidic networks, plasma dynamics, and corrosion chemistry.