The use of resonant whispering gallery modes (WGMs) for sensing exhibits various drawbacks and critical points related to the microsphere and tapered optical fiber fabrication tolerance. The uncertainty on the fiber taper and microsphere geometry or the gap between the microsphere and the fiber taper can complicate or limit the actual use of these devices for sensing, requiring peculiar calibration of the WGM based sensing set-up. An alternative double-step approach is proposed in this paper. In particular, the geometrical parameters of the set-up are recovered preliminarily and then the rare earth parameters are recovered via simple transmittance/gain measurements. The method is based on a refined electromagnetic model of the device suitably integrated with a particle swarm optimization (PSO) approach. The percent errors made on the up-conversion coefficients Cup and C3 are extremely low, being 0.75%, 0.05%, respectively. The procedure is very robust. It can be applied more in general, allowing the sensing of other physical parameters via simple transmittance measurements instead of wavelength shift ones, in both microsphere and microbubble based set-up.