This thesis addresses the 2-dimensional scanning probe microscope (SPM) lithography by scratching the sampling surface. The previous research has shown that servo controller has significant effect on the lithography. Carefully designed controller achieves more uniform scratch marks. This research has demonstrated that many unexpected effect can be observed when marking multiple lines. The material on the sample surface piles up on the sides of the plow mark. The plow mark would then become uneven when one tries to widen the ditch. The study also shows that it is possible to achieve more even marking geometry by carefully operate the cutting procedure. A Mu-synthesis controller is also presented to show how the outcome performance can be incorporated at the design stage. The experimental results confirm the design specifications.