Nanotechnology is revolutionizing human's life. Synthesis and application of magnetic nanoparticles is a fast burgeoning field which has potential to bring significant advance in many fields, for example diagnosis and treatment in biomedical area. Novel nanoparticles to function efficiently and intelligently are in desire to improve the current technology. We used a magnetron-sputtering-based nanocluster deposition technique to synthesize magnetic nanoparticles in gas phase, and specifically engineered nanoparticles for different applications.Alternating magnetic field heating is emerging as a technique to assist cancer treatment or drug delivery. We proposed high-magnetic-moment Fe3Si particles with relatively large magnetic anisotropy energy should in principle provide superior performance. Such nanoparticles were experimentally synthesized and characterized. Their promising magnetic properties can contribute to heating performance under suitable alternating magnetic field conditions. When thermal energy is used for medical treatment, it is ideal to work in a designed temperature range. Biocompatible and "smart" magnetic nanoparticles with temperature self-regulation were designed from both materials science and biomedicine aspects. We chose Fe-Si material system to demonstrate the concept. Temperature dependent physical property was adjusted by tuning of exchange coupling between Fe atoms through incorporation of various amount of Si. The magnetic moment can still be kept in a promising range. The two elements are both biocompatible, which is favored by in-vivo medical applications. A combination of "smart" magnetic particles and thermo-sensitive polymer were demonstrated to potentially function as a platform for drug delivery. Highly sensitive diagnosis for point-of-care is in desire nowadays. We developed composition- and phase-controlled Fe-Co nanoparticles for bio-molecule detection. It has been demonstrated that Fe70Co30 nanoparticles and giant magnetoresistance sensor make a successful integrated system for bio-molecule detection. In addition, we proposed the concept of "magnetic coloring": magnetic nanoparticles with different M-H loop form an archive of labels for detection of multiple molecules in the same sample. The composition- and phase- controlled Fe-Co particles are candidate to serve this application. Magnetic nanoparticles can also play a role in "green" catalysis. We synthesized core-shell structured nanoparticle with core rich in Fe, and shell rich in FeSiO, which have capability for phtocatalysis and magnetic recycling. The magnetic core enables recycling of catalysts by applying an external magnetic field. The shell shows good optical absorption which indicates the possibility of phtocatalysis. A big challenge for nanoparticles synthesized in gas phase is to transfer them into aqueous environment, especially in biomedical field. We experimented different approaches to modify the surface of magnetic nanoparticles. A direct way was developed to introduce functional molecule onto the surface of nanoparticles in vacuum. A new design of nanoparticle collection was implemented to assist surface modification in vacuum and to enable large quantity of manufacturing.