We propose a new approach to the modular packaging of microfluidic components, in which different functional components are not only fabricated separately but are also designed to be individually removable for the purposes of replacement or subsequent analysis. In this paper, we demonstrate one such component: a stand-alone microfluidic filter that can be custom-fabricated and then connected, disconnected, and replaced on a microfluidic chip as needed. This filter is also designed such that particles captured on the filter can be further analyzed or processed directly on the filter itself—for example, for microscopic examination or cell culturing. The filter is a thin (1 μm) transparent silicon nitride membrane that can be designed and fabricated according to specifications for different applications. This material is suitable for microscale fabrication; filtration of a variety of solutions, including biological samples; and subsequent particle imaging and processing. The porous nature of the thin filter allows for particle separation under relatively low pressures, thus protecting the particles from rupture or membrane damage. We describe two methods for integrating the filter apparatus onto a microfluidic chip such that it can be inserted, removed, and replaced. To demonstrate the utility of this approach, we fabricated custom-designed silicon-based filters, incorporated them onto microfluidic systems then filtered microparticles and live cells from test solutions, and finally removed the filters to image the microparticles and culture the cells directly on the filter membranes.