Microsurface scale characteristics (roughness, waviness and form) and the workpiece mounting fixture effects must be accounted and compensated for during laser micromachining such that the focused laser spot position is known in the coordinates of the measured surfaces. Thus, allowing rapid and accurate micromachining on the true workpiece engineering surface. The thin-plate splines (TPSs), a mathematically simple theory, is modified and employed in the reconstruction of 2 1/2 D unfolded continuous and differentiable microtopographical surfaces from a limited set of sampled digital elevation data. The TPS theory aids in restoring bad samples and in enhancing the visualization of the reconstructed surface and the characterization of microelectromechanical systems (MEMS) structures. The reverse engineered surface could also be interfaced and used with a CAD/CAM system to compensate for the focal spot location of a laser beam based on the actual reversed engineered workpiece surface. The practical examples of the real microsurfaces presented in this work, combine comprehensive identification with the ultimate goal of utilizing the algorithms in the compensation of the laser focused spot for a femtosecond laser micromachining (FLM) system currently under development in our laboratory.