This thesis is concerned with the task of autonomous selection of objects to remove (unload) them from a pile in robotic manipulation systems. Applications such as the automation of logistics processes and service robots require an ability to autonomously manipulate objects in the environment. A collapse of a pile of objects due to an inappropriate choice of the object to be removed from the pile cannot be afforded for an autonomous robotic manipulation system. This dissertation presents an indepth analysis of the problem and proposes methods and algorithms to empower robotic manipulation systems to select a safe object from a pile elaborately and autonomously. The contributions presented in this thesis are three-fold. First, a set of algorithms is proposed for extracting a minimal set of high level symbolic relations, namely, gravitational act and support relations, of physical interactions between objects composing a pile. The symbolic relations, extracted by a geometrical reasoning method and a static equilibrium analysis can be readily used by AI paradigms to analyze the stability of a pile and reason about the safest set of objects to be removed. Considering the problem of undetected objects and the uncertainty in the estimated poses as they exist in realistic perception systems, a probabilistic approach is proposed to extract the support relations and to make a probabilistic decision about the set of safest objects using notions from machine learning and decision theory. Second, an efficient search based algorithm is proposed in an internal representation to automatically resolve the inter-penetrations between the shapes of objects due to errors in the poses estimated by an existing object detection module. Refining the poses by resolving the inter-penetrations results in a geometrically consistent model of the environment, and was found to reduce the overall pose error of the objects. This dissertation presents the concept of minimum translation search for object pose refinement and discusses a discrete search paradigm based on the concept of depth of penetration between two polyhedrons. Third, an application centric evaluation of ranging sensors for selecting a set of appropriate sensors for the task of object detection in the design process of a real-world robotics manipulation system is presented. The performance of the proposed algorithms are tested on data sets generated in simulation and from real-world scenarios.