In this paper, we present the design and fabrication of 3-D silicon micro-arrays consisting of a wide range of isotropically-etched cavities and describe a model based upon their shape to investigate the influence of the etched features on cell trapping within cavities. We performed our study using non-invasive (MCF10A) and invasive (MDA-MB-231) breast cells separately and in a co-culture system. Our results indicate that with the etched surface ratio of ∼65%, it is possible to capture at least 80% of the cells within cavities in the silicon chip. The novel aspect of the proposed approach is that by changing the geometrical pattern of the etched features, it is possible to place the cells into the high density arrays with a desired capturing efficiency. In addition, it is not required to perform any coating or modification of the surface chemistry of the silicon substrate. The presented microstructures can be used as platforms for cell sorting, optical characterization, and basic biological studies.