It sounds to me like your in search of a non closed loop system? i.e. the indexer has no effect on the optical focus. If so there are a couple of things you need to think about. There are two different types of encoders, absolute and incremenental. Using an incremental encoder to determine absolute position requires a mechanical method to establish a "home" or absolute location. If you are talking of closing the loop with a stepper and encoder, then this becomes more problematic if rates of acceleration and motion are involved.
Phil, Still too many interests, too many projects, and not enough time!!!!!!!!
Vist my websites - http://pminmo.com & http://millpcbs.com