A tube handling system with a semi-automatic lab tube selection apparatus for enabling a user to pick a select lab tube in a standard lab tube holding rack with open-bottom wells that contain one or more lab tubes that includes a tube selection unit having, a housing with a top deck having a tube rack support, a transport mechanism contained within the housing having a carriage assembly, with the carriage assembly having a carrier with a push-pin, a drive system that moves the carrier and the push-pin under the tube rack support, and an actuator that raises the push-pin on command for removal, and, a control system to locate the carrier and the push-pin at a select location corresponding to a selected position under an open-bottom well of a tube rack positioned on the tube rack support to raise the push-pin for removal.