A method enables an operator to detect misalignment of printheads that eject clear ink in an inkjet printer. The method prints a first test pattern with a first color of ink and then prints a second test pattern of clear ink on top of the first test pattern. The ink of the first and the second test patterns is then spread to enable the clear ink to be dispersed in interstitial spaces in the ink of the first color. An operator is then able to detect the spatial relationship of predetermined marks in the second test pattern to predetermined marks in the first test pattern. The predetermined marks of the first and the second test patterns are arranged to enable an operator to detect a misalignment distance and the inkjet printer uses the misalignment distance entered by the operator to adjust the alignment of the printheads that eject clear ink.