A material modification assembly comprises an energy source for generating light beams to modify a substrate. A computing device generates pattern script(s) based on at least one parameter of the modification. The computing device also generates process script(s) including a type of pulse scripts to be used with the light beams and are based on at least one parameter of the interaction between the energy source and the substrate. The computing device combines the pattern script(s) with the process script(s) and generates command signals based on the combination. The computing device transmits the command signals to one or more additional devices of the material modification assembly to facilitate modifying the light beams for the modification to the substrate such that the modification includes a pattern on at least a surface of the substrate having dimensions and includes two or more discrete material alterations or changes spatially overlapped within the pattern.