Emulsions are widely used to produce sol–gel, drugs, synthetic materials, and food products. Recent advancements in microfluidic droplet emulsion technology has enabled the precise sampling and processing of small volumes of fluids (picoliter to femtoliter) by the controlled viscous shearing in microchannels. However the generation of monodispersed droplets smaller than 1 µm without surfactants has been difficult to achieve. Normally, the generation of satellite droplets along with parent droplets is undesirable and makes it difficult to control volume and purity of samples in droplets. In this paper, however, several methods are presented to passively filter out satellite droplets from the generation of parent droplets and use these satellite droplets as the source for monodispersed production of submicron emulsions. A passive satellite droplet filtration system and a dynamic satellite droplet separation system are demonstrated. Satellite droplets are filtered from parent droplets with a two-layer channel geometry. This design allows the creation and collection of droplets that are less than 100 nm in diameter. In the dynamic separation system, satellite droplets of defined sizes can be selectively separated into different collecting zones. The separation of the satellite droplets into different collecting zones correlates with the cross channel position of the satellite droplets during the breakup of the liquid thread. The delay time for droplets to switch between the different alternating collecting zones is nominally 1 min and is proportional to the ratio of the oil shear flows. With our droplet generation system, monodispersed satellite droplets with an average radius of 2.23 ± 0.11 µm, and bidispersed secondary and tertiary satellite droplets with radii of 1.55 ± 0.07 µm and 372 ± 46 nm respectively, have been dynamically separated and collected.