Methods for transferring substrates in a system with a factory interface robot between at least one FOUP, a buffer coupled to a parasitic device and an inbound and outbound transfer station coupled to a processing tool are provided. In one embodiment, a method for transferring substrates includes transferring a first substrate on an end effector of a robot from a FOUP to a buffer station serving a parasitic device, moving the substrate from the buffer station into the parasitic device, picking up a second substrate on the end effector, compensating for a residence time of the first substrate in the parasitic device, transferring the second substrate to parasitic device from the end effector to the buffer station serving the parasitic device, and picking up the first substrate from the buffer station.