Smart multifunctional magnetic nanoparticles are popular candidates for several biological applications owing to their intrinsic magnetic property and diverse applications that range from rare protein separation and biomedical utilization to cancer therapy and diagnostics. A universal protocol, for the development of such nanocarriers, is highly desirable for scientists with different backgrounds so that custom-made multifunctional nanoparticles can be developed to address their needs, among which are the superparamagnetic iron oxide and manganese oxide nanoparticles that are synthesized through high temperature decomposition reactions. However, an interface is needed to present these inorganic materials to biomolecules to enhance their application for different biological use. This compatibility is achieved by introducing a class of multifunctional copolymers. Magnetic nanoparticles are elaborately decorated with copolymers that carry three principle functionalities as follows: (1) dopamine moieties for surface anchorage of metal oxides; (2) dyes for optical detection; and (3) a large variety of functional molecules such as amines or carboxylates for conjugation of various biomolecules (i.e., proteins, nucleic acids, enzymes, etc.). These copolymers, in combination with nanoparticles, serve as a tool box that results in engineered nanotools with customized modifications and functionalities for applications in fields ranging from proteomics -bioseparation to tumor therapy.