Atomic force microscopes (AFM) provide high resolution images of surfaces. In this paper, we focus our attention on an inter ferometry method for deflection estimation of cantilever arrays in quasi-static regime. In its original form, spline interpolation was used to determine interference fringe phase, and thus the deflections. Computations were performed on a PC. Here, we propose a new complete solution with a least square based algorithm and an optimized FPGA implementation. Simulations and real tests showed very good results and open perspective for real-time estimation and control of cantilever arrays in the dynamic regime.