There is a need in many fields of science such as biology and biochemistry for systems which can integrate detection, analysis, and separation of complex mixtures. For biological samples, such as proteins, capillary electrophoresis (CE) has been used towards this end. When compared to competing methods, CE provides excellent separation efficiency and works well with very small injection volumes. Collection of samples post electrophoresis, however, has traditionally been challenging as analytes separate in compact pico/nanoliter size zones. Motivation to collect fraction can come from the desires to recover a rare sample and/or to keep separated components pure and concentrated post analysis. To address the problem of fraction collection, I have developed, and will present, a microfluidic platform, which incorporates a miniaturized CE system in series with a droplet generation device to encapsulate separated fractions post electrophoretic separation. In using inexpensive and readily available chromatography parts (e.g. tubing, unions, fittings) I have been able to engineer a capillary electrophoresis separation system which is capable of performing all basic capillary electrophoretic separations. Once the sample is electrophoresed, separated analytes are directed into a stream of silicon oil and form discrete nanoliter sized droplets. Through tuning the sample plug size, CE separation conditions, and rate of droplet formation, each analyte can be contained in a discrete number of droplets. The analytes can remain focused and isolated within their droplets indefinitely in the outlet tubing of the device. The preserved microenvironment of the droplets allows further sample manipulation, through the addition of reagents, targeted extraction, as well as further detection/analysis of the droplet components. For example, the isolated droplet can mix with reagents to reveal the identification of the analytes contained within. The presented platform uniquely combines the strengths of CE with the benefits of microfluidic design in a way that opens up new possibilities for post column studies and detection schemes.