Any recommendations on how can I process my AAV samples?

There are many different protocols on how to process AAV samples. We would recommend trying the procedures described in our application notes:

A duplex assay for quantification and qualification of adeno-associated virus (AAV) using the QIAcuity^® Digital PCR System
Optimized in-process recombinant adeno-associated virus (rAAV) vector genome titer protocol using the QIAcuity Digital PCR System