A system includes a cutting station having a laser cutter for cutting surface marks, score lines, holes, slots, flaps, panels, etc. into a selected substrate, an image capture device for capturing digital image data associated with the selected substrate, and a computing system for controlling the cutting process. The computing system 32 initiates a calibration test cycle that 1) cuts a test pattern into the selected substrate; and 2) analyzes the test pattern that was cut into the selected substrate. Based on the results of the analysis of the captured image, the system adjusts the operational parameters of the laser cutter during a subsequent packaging production run utilizing the same substrate type.