In an earlier paper, we applied configurational expressions of the temperature to the calculation of temperature profiles within a confined atomic fluid. This paper focuses on the application of these expressions to confined molecular fluids using ethane and hexane as examples. We first give configurational expressions for the temperature for these constrained systems. The configurational temperature profiles so obtained are compared to the kinetic temperature calculated using the equipartition principle, in equilibrium systems. These expressions are then used in nonequilibrium molecular dynamics (NEMD) simulations of fluids undergoing planar Poiseuille flow. We show that these configurational expressions provide a direct and accurate determination of the temperature profile for these systems.