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We present theoretical study and numerical simulation of Marangoni convection within ellipsoidal isotropic droplets embedded in free standing smectic films (FSSF). The thermocapillary flows are analyzed for both isotropic droplets spontaneously formed in FSSF overheated above the bulk smectic-isotropic transition, and oil lenses deposited on the surface of the smectic film. The realistic model, for which the upper drop interface is free from the smectic layers, while at the lower drop surface the smectic layering still persists is considered in detail. For isotropic droplets and oil lenses this leads effectively to a sticking of fluid motion at the border with a smectic shell. The above mentioned asymmetric configuration is realized experimentally when the temperature of the upper side of the film is higher than at the lower one. The full set of stationary solutions for Stokes stream functions describing the Marangoni convection flows within the ellipsoidal drops were derived analytically. The temperature distribution in the ellipsoidal drop and the surrounding air was determined in the frames of the perturbation theory. As a result the analytical solutions for the stationary thermocapillary convection were derived for different droplet ellipticity ratios and the heat conductivity of the liquid crystal and air. In parallel, the numerical hydrodynamic calculations of the thermocapillary motion in the drops were performed. Both the analytical and numerical simulations predict the axially-symmetric circulatory convection motion determined by the Marangoni effect at the droplet free surface. Due to a curvature of the drop interface a temperature gradient along its free surface always persists. Thus, the thermocapillary convection within the ellipsoidal droplets in overheated FSSF is possible for the arbitrarily small Marangoni numbers.