Contrary to popular belief, despite decades of research in fingerprints, reliable fingerprint recognition is still an open problem. Extracting features out of poor quality prints is the most challenging problem faced in this area. This paper introduces a new approach for fingerprint enhancement based on Short Time Fourier Transform(STFT) Analysis. STFT is a well known technique in signal processing to analyze non-stationary signals. Here we extend its application to 2D fingerprint images.The algorithm simultaneously estimates all the intrinsic properties of the fingerprints such as the foreground region mask, local ridge orientation and local frequency orientation. We have evaluated the algorithm over a set of 800 images from FVC2002 DB3 database and obtained a 17% relative improvement in the recognition rate.