Digital Holographic Microscopy enables single shot capture of Quantitative Phase images. In many cases the object under investigation is moving rapidly forcing a low exposure time. The result of this is a strong shot noise signal in the hologram plane which in turn results in a strong complex noise term in the reconstruction plane. The phase of the reconstructed image can be significantly effected with a speckle like noise which prevents efficient unwrapping. In this paper we demonstrate the application of Windowed Fourier Transform Filtering in order to reduce this noise in the phase image. The algorithm is implemented on a GPU and applied to images obtained from a commercial Digital Holographic Microscope. Â© 2012 OSA.