The present invention is directed to a system and method for establishing and/or maintaining proper alignment of a transfer mechanism. More specifically, the present invention is directed to an alignment system and method having one or more of: (a) a laser alignment device operable to providing precise locational coordinates for alignment of a robotic transfer mechanism relative to a holding structure; (b) an alignment tool for aligning a laser alignment device relative to robotic transfer mechanism; (c) lead in ramps to properly guide an individual specimen container into a holding well; and/or (d) a belt tensioning device for maintaining proper tension on one or more timing belts.