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This paper presents an optimization model for antenna selection and deployment in ceiling mounted, single and multi-cell RFID systems. The proposed model utilises a three-dimensional (3D) antenna radiation pattern, taking into consideration of both antenna half power beam width and downtilt angle. Specifically, we have analysed the effects of cell structures on detection probability in single-cell operation and signal-to-interference ratio (SIR) in multi-cell scenario. Four cell structures have been studied, namely, triangular cells, conventional rectangular cells, offset rectangular cells and hexagonal cells. Several design examples are also presented to show how to use this model to find the optimal configuration to cover the maximum area with a minimum number of antennas for a single cell scenario, as well as the trade-offs that have to be made to achieve a reasonable SIR in multi-cell operation. We believe this optimization model provides new insights into the optimal deployment of single and multi-cell RFID systems.