Printing systems are disclosed that produce homogenous, smooth edged printed patterns (such as integrated circuit (IC) patterns) by separating pattern layouts into discrete design layers having only parallel layout features, and by printing each design layer using individual print solution droplets deposited onto the substrate. A printhead alignment operation includes printing a first spot from a first printhead ejector on a first substrate location, positioning a second ejector over the first substrate location and printing a second spot, measuring a distance between the first spot and the second spot, adjusting a rotational orientation between the print head and the substrate to reduce the distance between the first spot and the second spot, and then repeating the printing, measuring and adjusting processes until the first and second spots are separated by a predefined threshold value apart. The design layers are then printed.