A two-dimensional transient analysis of the conjugate optical-thermal fields induced in a multilayer thin film structure on a glass substrate by a moving Gaussian laser source is carried out numerically. The workpiece is considered semi-infinite along the motion direction and its optical and thermophysical properties are assumed temperature dependent. The COMSOL Multiphysics 3.3 code has been used to solve the combined thermal and electromagnetic problem. The optical field is considered locally one dimensional and Maxwell equations are solved in order to evaluate the absorption in thin film. Results, in terms of transient temperature profiles and fields, are presented for different Peclet numbers and starting point of the heat source with respect to the workpiece boundary along the motion direction.