If you apply enough pre-stress then the frequencies will be different from the frequencies for the unstressed beam.

The guidelines given in your link explain HOW to set up and run the analysis, but I think you also need to understand WHY. The case described in the guidelines is for the vibration of a rotating blade. Under rotation, centripetal forces applied to the blade and put it into tension. The amount of tension depends on the mass density of each element in the blade and its distance from the axis of rotation - this is a very difficult problem.

If your problem is just a beam with a fixed boundary at one end and an applied force at the other, then your job will be easier. Many of the instructions will not be necessary for your job.

Perhaps it would be worthwhile having a thought experiment to help you decide what is important in your project? Consider a guitar or a piano. The strings are thick wires, and you could consider them to be beams. When you increase the tension, the frequency of the plucked strings increases. For long thin strings, the frequency is 2nd order (string tension rather than beam tension behaviour). For the very low notes of the piano, the wires are so thick that the 4th order Timoshenko beam behaviour becomes important (this creates a musical dissonance with the upper harmonics which means that the piano is tuned in a rather special way).

Thank you for the answer. It is helpful. Our case is simple; wherein we want to perform modal analysis of cantilever beam (thick and later thin) with an axial load. I wanted to know the procedure to do this in APDL.