Digital holography is widely used for the fast and accurate reconstruction of objects and 3D-scenes characteristics: intensity, depth locations, density, temperature, refractive index, etc. There are various types of noise in digital holography, including speckle noise, zero order and twin image, camera shot noise and fixed-pattern noise. Therefore, additional hologram processing is required to obtain a high-quality reconstructed image. This paper proposes an optical-digital method of noise suppression in digital holography. First, a set of uncorrelated holograms is registered. The reconstructed images are treated as a 3D array, to which a 3D filter is then applied. A 3D median filter is used in this study; however, other 3D filters based on weighted average can be utilized also. The proposed method was verified using computer-generated and optically registered digital Fresnel holograms. Even with a small number of images, the method significantly improves the quality: the normalized standard deviation was decreased by up to 3-10 times and speckle contrast was reduced by more than six times. Registration of only ten holograms is sufficient to obtain a quality close to the maximum. The flexibility of the proposed method allows for varying the ratio of the reconstruction quality to the processing time.