In this article, a reliable method for surface topography is proposed employing a digital holographic microscopy setup. The proposed method is based on extracting the surface profile from the phase map encoded in the hologram signal. For hologram acquisition and reconstruction, we used a Raspberry Pi computer and camera module in our experimental setup, which is a step toward low-cost non-contact surface profilometry. A graphics processing unit (GPU) assisted state space method is used for rapid and reliable phase estimation, providing high robustness against noise. The experimental finding for a standard calibration target corroborates the practical viability of the proposed method.