Here we describe a fully automated PCR purification method using Millipore’s Montage* PCR₉₆ Cleanup Kit on the Beckman Biomek FX pipettor. The procedure requires no manual intervention after the deck is set up. The process was set up on an instrument with one 96 channel pipetting head and one vacuum manifold on the deck. To increase the throughput of this process, the deck can be set up with four vacuum manifolds to handle multiple plates simultaneously. Purification conditions may be optimized for individual needs. The protocol includes one filtration step followed by resuspension and recovery of the sample in a volume to be specified by the user. The procedure yields 1 plate of 96 purified products in less than 15 minutes.