You can reprogram any of the buttons and use the learning function off the original remote.
So if your original remote had a button for an app you want to use then just pair that button up with say the Netflix button on this one. But if you mean program the Netflix/Prime buttons to other apps installed on your TV, then you'd have to somehow associate your original TV's remote Netflix/Prime video button to load the alternative app as all it's doing is sending that same IR code to the TV to do that same function since all but the pre-programmed TV apps themselves don't have a specific IR code if that makes sense so the TV would have to have the capability to allow you to remap the buttons to load a new app instead of what has been pre-defined for that button on the original remote.