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This study proposed an auto focusing method for a multi-focus image in assembling lens modules in digital camera phones. A camera module in a camera phone is composed of a lens barrel, an IR glass, a lens mount, a PCB board and aspheric lenses. Alignment among the components is one of the important factors in product quality. Auto-focus is essential to adjust image quality of an IR glass in a lens holder, but there are two focal points in the captured image due to thickness of IR glass. So, sharpness, probability and a scale factor are defined to find desired focus from a multi-focus image. The sharpness is defined as clarity of an image. Probability and a scale factors are calculated using pattern matching with a registered image. The presented algorithm was applied to a lens assembly machine which has 5 axes, two vacuum chucks and an inspection system. The desired focus can be determined on the local maximum of the sharpness, the probability and the scale factor in the experiment.