This paper addresses the three-dimensional scanning probe microscopy (SPM). The previous research has shown that the servo controller imposes significant effect on the lithography. A good controller enables a uniform and precise lithography pattern. This research, as a continuation to the previous work, achieved three-degree-of-freedom control of the SPM PZT driver and was able to scratch various patterns on the sample such as lines, flats and pyramids with different algorithms. This research also demonstrated that many unexpected effect could be observed when conducting continuous marking. The debris piles up on the sides of the plow mark and is very difficult to clean. It is also demonstrated that cleaning the debris by repetitively scratching the surface is possible. In addition, the design procedure for a Mu-synthesis controller is also presented to achieve desired performance. The experimental results confirm the design specifications.