Aqueous solution droplets are supported quasi contact-free by superhydrophobic surfaces. The convective flow in evaporating droplets allows the manipulation and control of biological molecules in solution. In previous works, super-hydrophobic drops on nano-patterned substrates have been used to analyze otherwise undetectable species in extremely low concentration ranges. Here, we used particle image velocimetry (PIV) for studying the flow field in water droplets containing polystyrene particles on a pillared silicon super-hydrophobic chip. The particles describe vortex-like motions around the droplet center as long as the evaporating droplet maintains a spherical shape. Simulations by a Finite Element Method (FEM) suggest that the recirculating flow is due to the temperature gradient along the droplet rim, generating a shear stress. Notably, the characteristics of the internal flow can be modulated by varying the intensity of the temperature gradient along the drop. We then used the flow-field determined by experiments and an approximate form of the Langevin equation to examine how particles are transported in the drop as a function of particle size. We found that larger particles with an average size of 36 μm are preferentially transported toward the center of the substrate, differently from smaller particles with a 10-fold lower size that are distributed more uniformly in the drop. Results suggest that solutions of spherical particles on a super-hydrophobic chip can be used to separate soft matter and biological molecules based on their size, similarly to the working principle of a time-of-flight (ToF) mass analyzer, except that the separation takes place in a micro-sphere, with less space, less time, and less solution required for the separation compared to conventional ToF systems.