We introduce a microfluidic platform that combines hydrodynamic trapping and magnetic switching techniques for precise manipulating magnetic micro-particles and forming particle and cell arrays, in a massively parallel manner. In the first step, hydrodynamic forces transport and then trap the single particles and cells in a large array. Then, magnetic forces transfer them into adjacent low-shear compartments which are used as single cell culture micro-chambers. Furthermore, using this tool, we run single cell assays and perform drug screening as well as mRNA analysis experiments. The flawless magnetic transport in this work is obtained by growing a non-fouling layer on microchannel surfaces. The chip treatment became possible by a novel microfluidic chip design and a new simple self-aligned fabrication method, based on a silicon substrate, magnetic nano thin-films embedded in the microfluidic walls, and a glass lid. The resulting chip is an innovative tool suitable for long-term single cell phenotypic and genotypic studies, with applications in immunology and medicine.