An improved apparatus for positioning and aligning a patterned surface of a semiconductor structure directly opposite to solder filled patterned mold cavities of a mold structure includes a pattern based alignment too including means for identifying a mold training pattern image and a semiconductor training pattern image on a training mold structure and a training semiconductor structure, respectively, means for training the alignment tool with the training pattern images, means for storing the alignment tool trained position, means for identifying a mold pattern image and a semiconductor pattern image on the mold structure and the semiconductor structure matching the mold training pattern image and the semiconductor training pattern image, respectively, and means for aligning the identified mold pattern image with the semiconductor pattern image.