The morphology, structure, and magnetic properties of Fe3O4 and Fe3O4@C nanoparticles, as well their effectiveness for organic dye adsorption and targeted destruction of carcinoma cells, were studied. The nanoparticles exhibited a high magnetic saturation value (79.4 and 63.8 emu/g, correspondingly) to facilitate magnetic separation. It has been shown that surface properties play a key role in the adsorption process. Both types of organic dyes—cationic (Rhodomine C) and anionic (Congo Red and Eosine)—were well adsorbed by the Fe3O4 nanoparticles’ surface, and the adsorption process was described by the polymolecular adsorption model with a maximum adsorption capacity of 58, 22, and 14 mg/g for Congo Red, Eosine, and Rhodomine C, correspondingly. In this case, the kinetic data were described well by the pseudo-first-order model. Carbon-coated particles selectively adsorbed only cationic dyes, and the adsorption process for Methylene Blue was described by the Freundlich model, with a maximum adsorption capacity of 14 mg/g. For the case of Rhodomine C, the adsorption isotherm has a polymolecular character with a maximum adsorption capacity of 34 mg/g. To realize the targeted destruction of the carcinoma cells, the Fe3O4@C nanoparticles were functionalized with aptamers, and an experiment on the Ehrlich ascetic carcinoma cells’ destruction was carried out successively using a low-frequency alternating magnetic field. The number of cells destroyed as a result of their interaction with Fe3O4@C nanoparticles in an alternating magnetic field was 27%, compared with the number of naturally dead control cells of 6%.