The Fast Multi-Channel Photonics Alignment system (FMPA) design is based on a highly specialized digital motion controller (E-712) and a hybrid alignment mechanism to achieve the required long travel ranges without sacrificing stability, resolution or alignment speed. FMPA is implemented in the E-712’s modular firmware to enable fast, simultaneous alignment and tracking of multi-channel couplings in multiple degrees of freedom. A broad variety of coarse/fine mechanisms can be used, enabling a spectrum of applications from undiced wafer to final package. Long-travel, closed-loop piezo nanopositioners ensure high throughput and reliable reproducibility. High-precision stage stack or hexapod options accommodate any application up to 6 DOFs per coupling.