A magnetic encoder scale having a series of periodically spaced magnetic marks. A reference mark is applied to the scale using an applicator or template, which has a feature for locating the reference mark. The applicator or template has one or more magnetic marks corresponding to the periodic scale marks, whereby the applicator or template automatically assumes a defined phase relationship relative to the periodic scale marks when placed on the scale. The reference mark may be attached to the scale self-adhesively, or it may be formed by removal of material from the scale, guided by the applicator or template. The applicator may alternatively have a strong permanent magnet which applies further magnetization to a region of the scale.