A floor isolation system installed in a single floor or room in a fixed base structure is designed to protect equipment. With this configuration, the input motions to the floor isolation from the ground motions are filtered by the structure, leaving the majority of the frequency content of the input motion lower than the predominant frequency of the structure. The floor isolation system should minimize the acceleration to protect equipment; however, displacement must also be limited to save floor space, especially with long period motion. Semi-active control with an control was adopted for the floor isolation system and a new input shaping filter was developed to account for the input motion characteristics and enhance the effectiveness of the control. A series of shake table tests for a semi-active floor isolation system using rolling pendulum isolators and a magnetic-rheological damper were performed to validate the control. Passive control using an oil damper was also tested for comparison. The test results show that the control effectively reduced acceleration for short period motions with frequencies close to the predominant frequency of the structure, as well as effectively reduced displacement for long period motions with frequencies close to the natural frequency of the floor isolation system. The control algorithm proved to be more advantageous than passive control because of its capacity to adjust control strategies according to the different motion frequency characteristics.