Theoretically, in electrospinning process, the amounts of target substance in the solution and the final product are the same, and presented either inside or on the surface of produced fibers. Therefore, you may be able to simply wash the surface of nanofibers using suitable solvents and then, measure the amount of target substance in that solvent to calculate the amount of target substance on the surface of nanofibers and finally, subtract it from total added amount to obtain the encapsulation efficiency.

If the fibers were collected on a dry collector, the polymer solution is completely transformed into fibers and some studies concludes on total encapsulation. One thing you can do is to weight and dissolve a part of your fibrous scaffold, in the proper solvent that can dissolve both your fibers and agent and try to measure encapsulation efficiency from specific peaks of your agent by using UV spectrophotometer (If posibble). If you collected your fibers in a bath collector, you can detect the unencapsulated agent as dissolved in the collector solvent and calculate the encapsulation efficiency.