We have done Extremities treatment with Align RT.
Mostly we still use a vac-loc, but as Elle already said; we make sure the side of this vac-loc are not high (but give a bit of support) in order to make sure the Align RT camera`s are gonna be able to detect also rotations.
Another tip which might help you, is to include a joint in the ROI, or something that is gonna help you define the longitudinal position of the patient. If you would use a middle part of the under limb for example, there is nothing for the system to detect where on the leg we would like to be.
What also could help you set-up the patient is to use the fuction of making a treatment capture. Here you can see big shifts/rotations.
Hopefully this will help you further!