You asked this question above.

if I give the displacement input with the fixed rotation at the faces fastened to the shaker within transient structural of ANSYS. Then I need to subtract the input displacement to get the relative displacement. If I am correct, then how could I give the displacement/acceleration signal to the mass. therefore I do not need to subtract the base displacement if I would like to probe the Z-direction response of the IC chip.

When you apply a displacement signal to the edges of the PCB clamped to the shaker, all the mass in the IC and PCB are connected to those faces so the stiffness of the PCB transfers the enforced displacement at the clamped edges to all the elemental masses in the structure. You don't give it anything else.

A node at the center of the free edge of the PCB might move differently to a node on the  IC and they both have a different relationship to the motion of the node clamped to the fixture which has the input displacement enforced on it.  When you probe the Z-direction of the node on the free edge, you subtract the Z-direction enforced displacement of the fixture.  Similarly, when you probe the Z-direction of the node on the IC, you subtract the Z-direction enforced displacement of the fixture.  You get two relative displacements: free edge of PCB and IC edge and you must have subtracted the base displacement to get this.