Accurate positioning of a sample is one of the primary challenges in laser micromanufacturing. There are a number of methods that allow detection of the surface position; however, only a few of them use the beam of the processing laser as a basis for the measurement. Those methods have an advantage that any changes in the processing laser beam can be inherently accommodated. This work describes a direct, contact-free method to accurately determine workpiece position with respect to the structuring laser beam focal plane based on nonlinear harmonic generation. The method makes workpiece alignment precise and time efficient due to ease of automation and provides the repeatability and accuracy of the surface detection of less than 1 μm.