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The primary objective of this thesis is to develop a general computational framework to perform large scale moving boundary problems in fluid mechanics. The interactions of moving entities with fluid flow are common to numerous engineering and biomedical applications. The novel computational platform developed comprises of a) an efficient fluid flow solver b) an accurate and easily implemented unified formulation to capture the interactions of the moving bodies with the flow and c) parallel execution capability to enable large scale computations. The above features are formulated and implemented in a computer code, ELAFINT3D. The current thesis demonstrates the accuracy, efficiency and robustness of this framework. The performance of ELAFINT3D on distributed memory systems is also presented. Finally, this framework is employed to simulate a series of large scale, three-dimensional moving boundary problems involving complex interfacial motions and flow phenomena. These numerical experiments establish the strengths of the current tool.