Embodiments of the present disclosure provide a mask structure and a filtered cathodic vacuum arc (FCVA) apparatus. The mask structure is configured to prepare protrusions on a carrying surface of an electrostatic chuck and includes a main mask plate and a side mask plate that are made of a conductive metal. The main mask plate is configured to form a patterned film layer corresponding to the protrusions on the carrying surface of the electrostatic chuck. The side mask is configured to cover a side surface of the electrostatic chuck to avoid forming a film layer on the side surface. The mask structure can be electrically conductive. The mask structure may prevent the side surface of the electrostatic chuck from being coated when the protrusions are prepared on the carrying surface of the electrostatic chuck. Thus, the mask structure may be applied to an FCVA process.