A system and process for compensating for non-uniform surfaces of a substrate when direct printing traces is provided. The system and process provided herein measures the surface of a substrate and can determine whether the surface is substantially flat, rises or falls, or whether a mesa or valley is encountered. Depending on the surface feature (i.e., mesa, valley, falling or rising surface), the direct printing system can change the frequency of the printing timing signal, advance or retard the print timing signal, advance or retard the print data, or make repeated passes over certain areas. In addition, the process disclosed herein can determine whether two, three or all of the aforementioned steps for compensating for non-uniform substrates should be combined to most effectively and efficiently print on the non-uniform surface of the substrate as intended.