The core structure of high-frequency terahertz (THz) filter has the characteristics of cross-scale, large removal and high precision. In order to realize efficient and precise machining of core structure, the choice of machining technology is particularly important. Compared with common machining, lithography and MEMS technology, the femtosecond laser machining technology has the advantages of strong universality of materials, simple machining flow and precision machining of thin-walled structures. The core structure of THz filter with center frequency of 850 GHz was designed as input, and the machining experiment of the core structure of THz filter was carried out by femtosecond laser machining technology. Considering that the femtosecond laser with low repetition rate could not meet the actual requirements of high-efficiency machining, the high-repetition-rate femtosecond laser was selected as the machining light source, and the high-efficiency and precise machining of the core structure of high-frequency THz filter was realized under the conditions of precise design of machining strategy and precise optimization of machining parameters. The results show that the measured center frequency of the THz filter fabricated by high-repetition-rate femtosecond laser is close to the designed value. Therefore, the high-repetition-rate femtosecond laser processing technology can be used as a flexible stage in the processing of the core structure of THz filter.