A method of characterizing and correcting effective radius variations in a surface nanoscale axial photonic (SNAP) device that comprises a plurality of separate optical microdevices includes the steps of characterizing an as-fabricated SNAP device to determine local effective radius values of the plurality of separate optical microdevices, calibrating the as-fabricated SNAP device to determine a correction factor defined as a change in effective radius associated with a predetermined corrective treatment and then correcting individual microdevices by the application of a number of refractive index-changing treatments, the number of treatments applied to individual microdevices determined by the amount of correction required and the correction factor determined in the calibrating step. A number of iterations of the characterizing and correcting operations can be performed, achieving less than an Angstrom variation in effective radius variation. An apparatus for performing the method is also disclosed.