Strong shock interaction with the boundary layer in high speed flows results in boundary layer separation. They are associated with low frequency oscillations of the separation shock whose origin has been a source of debate for many years. The inherent unsteadiness in the flow field has been extensively studied in the past decade for two-dimensional flows. But the unsteadiness associated with the 3-D flows has not yet been well understood. The present work aims at performing experiments to understand the dynamics of the unsteady shock using Schlieren visualization and separation region downstream the shock using surface oil flow visualization for the Mach 2.97 flow over a square protrusion. To compliment the experiments, computations are done using commercial CFD packages. The mean separation distance was observed to be at xsep/h = 2.33. With the study performed, strategic locations to place the pressure sensors can be identified to study the time series of unsteady pressure. © 2021, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.