Microfluidic processes are of great interest for the production of nanoparticles with reproducible properties. However, in real systems, it is difficult to completely exclude incidental production of larger particles, which can contaminate the product or clog downstream process modules. A class of microfluidic filters was devised for eliminating particulate contamination in multistage continuous-flow processes. To achieve high throughput and filtration efficiency, a high-surface-area filter with an application-adapted bonding method was developed. As a model application, the filtration efficiency was analyzed for lipid nanoparticles made by microfluidic antisolvent precipitation and the results were compared with requirements of the European and US guidelines.