The time evolution of planetary boundary layer can be studied from sodar data. Normally most of the sound wave transmitted above gets backscattered from a single inversion layer. However, during turbulent atmospheric conditions, there are multiple layers from where the signal gets backscattered with varying echo strengths. The present work describes a methodology for computer analysis of multilayered structures. Two distinct backscatter heights are extracted from observed echograms. This noisy measurement is filtered to estimate the layer heights using an a priori system model. The process and measurement noise covariances used by the filter algorithm are tuned from physical considerations to get good filter performance. Data from sodar installed at Maitree station of Antarctica with capping over an inversion layer is used to prove the concept.