Micro laser fabrication techniques can potentially be used for the manufacture of microstructures on the thin flat surfaces with large diameter that are frequently used in semiconductor industries. However, the large size of wafers can cause the degraded machining accuracy of the surface because it can be tilted or distorted by geometric errors of machines or the holding fixtures, etc. To overcome these errors the off-line focusing error compensation method is proposed. By using confocal autofocus system, the focusing error profile of machined surface is measured along the pre-determined path and can be compensated at the next machining process by making the corrected motion trajectories. The experimental results for silicon wafers and invar flat surfaces show that the proposed method can compensate the focusing error within the level of below $6.9{mu}m$ that is the depth of focus required for the laser micromachining process.