It depends on what you used for your encapsulation (if any). There are some filters that can separate excipients with different molecular weights.

If you can't seperate the oil droplets from the aqueous phase by centrifugation or ultrafiltration, you need any property of the drug which is different in oil and water, e.g. spectroscopic properties (UV, fluorescence, NMR, IR, Raman), dipole moment, conductivity, pH. If the diffence is large enough and the method is sensitive enough you can model the spectra by at least two different species (in water and oil), but you must be careful, because the surfactant (or any other component of the nanoemulsion) may change the property, too. Therefore several preliminary experiments in water, surfactant solution, oil and oil + surfactant and perhaps others are needed. Usally, at least in long-term, the solubility should not exceed the solubilty of the drug in surfactant solution that is in equilibrium with the oil. For a certain time after the preparation, it can be larger depending on the way you prepare the nanoemulsion.

Hi

Your formulation is a nano emulsion, you knew the drug quantity you added in the formulation, the aqueous and oily phases. By performing Raman Spectroscopy, we can find the concentration of drug in each phase, and then it would be easy to calculate the drug entrapped and free drug. Or try to do indirectly by phase inversion adding either of the phase in known excess quantities. Then the phases get separated, Do partition coefficient studies for each phase by collecting using a separating funnel. collect the individual phases and find out the concentration of drug present in each phase and finally you can calculate the free drug.