A method for correcting misalignment between a plurality of columns of color ink jetting nozzle arrays of a color printhead during printing with a hand held printer includes determining a misdirection angle of motion of the plurality of columns of color ink jetting nozzle arrays relative to a desired direction of motion of the hand operated printer; determining for each of the plurality of columns of color ink jetting nozzle arrays a respective usable nozzles subset to be used in printing a swath, based on the misdirection angle; determining an amount of shifting of at least one of the respective usable nozzles subsets to adjust for non-perpendicularity of the color ink jetting nozzle arrays relative to the desired direction of motion, based on the misdirection angle; and shifting the respective usable nozzles subset for a respective column based on the amount determined.