A method and system for calculating a control function for a structural system (10) that can be used to determine an appropriate control force to apply to an active member (18) within a stationary member (12) on the structural system (10). An active member (18) and a stationary member (12) are defined as a two-mass system in which the active member (18) and the stationary member (12) move in opposite directions. The stationary member (12) is mounted to an isolation subsystem (14) that is composed of six isolators (28) at multiple degrees of freedom. The isolation subsystem (14) is softer than the stationary member (12), active member (18) and a spacecraft surface (16) due to a damping element (32) of the isolation subsystem (16). The isolation subsystem (16) is mounted to the spacecraft (16) and decouples the spacecraft (16) from the stationary member (12) and thus the active member (18). An accurate control force for the active member (18) can be determined based upon the above structure (10).