There are several physics interfaces included in the Polymer Flow Module to model heat transfer and nonisothermal flow. These physics interfaces are found under the Heat Transfer branch () as well as those under the Fluid Flow > Nonisothermal Flow branch (). The Polymer Flow Module includes also the Laminar Flow version of the Rotating Machinery, Nonisothermal Flow multiphysics interface (), found under the Fluid Flow > Nonisothermal Flow > Rotating Machinery, Nonisothermal Flow branch ().

The basic functionality for simulating heat transfer in homogeneous media is described in Heat Transfer in the COMSOL Multiphysics Reference Manual.