The mode shapes and modal frequencies are obtained from solving for the eigenvalues and eigenvectors in the system of equations. A general explanation can be found here Wiki link
Yes, the modal frequencies represent the fundamental and harmonic resonant frequencies of the structure. The deformation values are arbitrary, and are used to represent the mode shapes. Structrual constraints and loads will affect the modal values and mode shapes. If not fixed, the first six modes will represent rigid body movements of the DOFs. To take account for the sturctural loads (pre-stressed modal) the appropriate checkbox needs to be set in the Simulation settings.
Hope this helps!
Best regards, -Hugh
Hugh Henderson
QA Engineer (Fusion Simulation)