The state-of-the-art object pose estimation approaches represent the set of detected poses together with corresponding uncertainty. The inaccurate noisy poses may result in a configuration of overlapping objects especially in cluttered environments. Under a rigid body assumption the inter-penetrations between pairs of objects are geometrically inconsistent. In this paper, we propose the principle of minimum translation search, PROMTS, to find an inter-penetration-free configuration of the initially detected objects. The target application is to automate the task of unloading shipping containers, where a geometrically consistent configuration of objects is required for high level reasoning and manipulation. We find that the proposed approach to resolve geometrical inconsistencies improves the overall pose estimation accuracy. We examine the utility of two selected search methods: A-star and Depth-Limited search. The performance of the search algorithms are tested on data sets generated in simulation and from real-world scenarios. The results show overall improvement of the estimated poses and suggest that depth-limited search presents the best overall performance.